diff --git a/scripts/manifest.py b/scripts/manifest.py
index 8cd53df..32603e8 100755
--- a/scripts/manifest.py
+++ b/scripts/manifest.py
@@ -23,6 +23,37 @@
 android_ns = 'http://schemas.android.com/apk/res/android'
 
 
+def get_or_create_applications(doc, manifest):
+  """Get all <application> tags from the manifest, or create one if none exist.
+  Multiple <application> tags may exist when manifest feature flagging is used.
+  """
+  applications = get_children_with_tag(manifest, 'application')
+  if len(applications) == 0:
+    application = doc.createElement('application')
+    indent = get_indent(manifest.firstChild, 1)
+    first = manifest.firstChild
+    manifest.insertBefore(doc.createTextNode(indent), first)
+    manifest.insertBefore(application, first)
+    applications.append(application)
+  return applications
+
+
+def get_or_create_uses_sdks(doc, manifest):
+  """Get all <uses-sdk> tags from the manifest, or create one if none exist.
+  Multiple <uses-sdk> tags may exist when manifest feature flagging is used.
+  """
+  uses_sdks = get_children_with_tag(manifest, 'uses-sdk')
+  if len(uses_sdks) == 0:
+    uses_sdk = doc.createElement('uses-sdk')
+    indent = get_indent(manifest.firstChild, 1)
+    manifest.insertBefore(uses_sdk, manifest.firstChild)
+
+    # Insert an indent before uses-sdk to line it up with the indentation of the
+    # other children of the <manifest> tag.
+    manifest.insertBefore(doc.createTextNode(indent), manifest.firstChild)
+    uses_sdks.append(uses_sdk)
+  return uses_sdks
+
 def get_children_with_tag(parent, tag_name):
   children = []
   for child in parent.childNodes:
diff --git a/scripts/manifest_check.py b/scripts/manifest_check.py
index c48c9f9..1e32d1d 100755
--- a/scripts/manifest_check.py
+++ b/scripts/manifest_check.py
@@ -25,10 +25,7 @@
 import sys
 from xml.dom import minidom
 
-from manifest import android_ns
-from manifest import get_children_with_tag
-from manifest import parse_manifest
-from manifest import write_xml
+from manifest import *
 
 
 class ManifestMismatchError(Exception):
@@ -205,15 +202,9 @@
     """Extract <uses-library> tags from the manifest."""
 
     manifest = parse_manifest(xml)
-    elems = get_children_with_tag(manifest, 'application')
-    if len(elems) > 1:
-        raise RuntimeError('found multiple <application> tags')
-    if not elems:
-        return [], [], []
-
-    application = elems[0]
-
-    libs = get_children_with_tag(application, 'uses-library')
+    libs = [child
+            for application in get_or_create_applications(xml, manifest)
+            for child in get_children_with_tag(application, 'uses-library')]
 
     required = [uses_library_name(x) for x in libs if uses_library_required(x)]
     optional = [
diff --git a/scripts/manifest_check_test.py b/scripts/manifest_check_test.py
index 7aaf8a9..abe0d8b 100755
--- a/scripts/manifest_check_test.py
+++ b/scripts/manifest_check_test.py
@@ -234,6 +234,32 @@
             optional_uses_libraries=['//x/y/z:bar'])
         self.assertTrue(matches)
 
+    def test_multiple_applications(self):
+        xml = """<?xml version="1.0" encoding="utf-8"?>
+            <manifest xmlns:android="http://schemas.android.com/apk/res/android">
+                <application android:featureFlag="foo">
+                    <uses-library android:name="foo" />
+                    <uses-library android:name="bar" android:required="false" />
+                </application>
+                <application android:featureFlag="!foo">
+                    <uses-library android:name="foo" />
+                    <uses-library android:name="qux" android:required="false" />
+                </application>
+            </manifest>
+        """
+        apk = self.apk_tmpl % ('\n'.join([
+            uses_library_apk('foo'),
+            uses_library_apk('bar', required_apk(False)),
+            uses_library_apk('foo'),
+            uses_library_apk('qux', required_apk(False))
+        ]))
+        matches = self.run_test(
+            xml,
+            apk,
+            uses_libraries=['//x/y/z:foo'],
+            optional_uses_libraries=['//x/y/z:bar', '//x/y/z:qux'])
+        self.assertTrue(matches)
+
 
 class ExtractTargetSdkVersionTest(unittest.TestCase):
 
diff --git a/scripts/manifest_fixer.py b/scripts/manifest_fixer.py
index 90e12e1..9847ad5 100755
--- a/scripts/manifest_fixer.py
+++ b/scripts/manifest_fixer.py
@@ -23,15 +23,7 @@
 from xml.dom import minidom
 
 
-from manifest import android_ns
-from manifest import compare_version_gt
-from manifest import ensure_manifest_android_ns
-from manifest import find_child_with_attribute
-from manifest import get_children_with_tag
-from manifest import get_indent
-from manifest import parse_manifest
-from manifest import write_xml
-
+from manifest import *
 
 def parse_args():
   """Parse commandline arguments."""
@@ -91,47 +83,33 @@
 
   manifest = parse_manifest(doc)
 
-  # Get or insert the uses-sdk element
-  uses_sdk = get_children_with_tag(manifest, 'uses-sdk')
-  if len(uses_sdk) > 1:
-    raise RuntimeError('found multiple uses-sdk elements')
-  elif len(uses_sdk) == 1:
-    element = uses_sdk[0]
-  else:
-    element = doc.createElement('uses-sdk')
-    indent = get_indent(manifest.firstChild, 1)
-    manifest.insertBefore(element, manifest.firstChild)
-
-    # Insert an indent before uses-sdk to line it up with the indentation of the
-    # other children of the <manifest> tag.
-    manifest.insertBefore(doc.createTextNode(indent), manifest.firstChild)
-
-  # Get or insert the minSdkVersion attribute.  If it is already present, make
-  # sure it as least the requested value.
-  min_attr = element.getAttributeNodeNS(android_ns, 'minSdkVersion')
-  if min_attr is None:
-    min_attr = doc.createAttributeNS(android_ns, 'android:minSdkVersion')
-    min_attr.value = min_sdk_version
-    element.setAttributeNode(min_attr)
-  else:
-    if compare_version_gt(min_sdk_version, min_attr.value):
+  for uses_sdk in get_or_create_uses_sdks(doc, manifest):
+    # Get or insert the minSdkVersion attribute.  If it is already present, make
+    # sure it as least the requested value.
+    min_attr = uses_sdk.getAttributeNodeNS(android_ns, 'minSdkVersion')
+    if min_attr is None:
+      min_attr = doc.createAttributeNS(android_ns, 'android:minSdkVersion')
       min_attr.value = min_sdk_version
-
-  # Insert the targetSdkVersion attribute if it is missing.  If it is already
-  # present leave it as is.
-  target_attr = element.getAttributeNodeNS(android_ns, 'targetSdkVersion')
-  if target_attr is None:
-    target_attr = doc.createAttributeNS(android_ns, 'android:targetSdkVersion')
-    if library:
-      # TODO(b/117122200): libraries shouldn't set targetSdkVersion at all, but
-      # ManifestMerger treats minSdkVersion="Q" as targetSdkVersion="Q" if it
-      # is empty.  Set it to something low so that it will be overridden by the
-      # main manifest, but high enough that it doesn't cause implicit
-      # permissions grants.
-      target_attr.value = '16'
+      uses_sdk.setAttributeNode(min_attr)
     else:
-      target_attr.value = target_sdk_version
-    element.setAttributeNode(target_attr)
+      if compare_version_gt(min_sdk_version, min_attr.value):
+        min_attr.value = min_sdk_version
+
+    # Insert the targetSdkVersion attribute if it is missing.  If it is already
+    # present leave it as is.
+    target_attr = uses_sdk.getAttributeNodeNS(android_ns, 'targetSdkVersion')
+    if target_attr is None:
+      target_attr = doc.createAttributeNS(android_ns, 'android:targetSdkVersion')
+      if library:
+        # TODO(b/117122200): libraries shouldn't set targetSdkVersion at all, but
+        # ManifestMerger treats minSdkVersion="Q" as targetSdkVersion="Q" if it
+        # is empty.  Set it to something low so that it will be overridden by the
+        # main manifest, but high enough that it doesn't cause implicit
+        # permissions grants.
+        target_attr.value = '16'
+      else:
+        target_attr.value = target_sdk_version
+      uses_sdk.setAttributeNode(target_attr)
 
 
 def add_logging_parent(doc, logging_parent_value):
@@ -147,37 +125,27 @@
   manifest = parse_manifest(doc)
 
   logging_parent_key = 'android.content.pm.LOGGING_PARENT'
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
+  for application in get_or_create_applications(doc, manifest):
+    indent = get_indent(application.firstChild, 2)
 
-  indent = get_indent(application.firstChild, 2)
-
-  last = application.lastChild
-  if last is not None and last.nodeType != minidom.Node.TEXT_NODE:
-    last = None
-
-  if not find_child_with_attribute(application, 'meta-data', android_ns,
-                                   'name', logging_parent_key):
-    ul = doc.createElement('meta-data')
-    ul.setAttributeNS(android_ns, 'android:name', logging_parent_key)
-    ul.setAttributeNS(android_ns, 'android:value', logging_parent_value)
-    application.insertBefore(doc.createTextNode(indent), last)
-    application.insertBefore(ul, last)
     last = application.lastChild
+    if last is not None and last.nodeType != minidom.Node.TEXT_NODE:
+      last = None
 
-  # align the closing tag with the opening tag if it's not
-  # indented
-  if last and last.nodeType != minidom.Node.TEXT_NODE:
-    indent = get_indent(application.previousSibling, 1)
-    application.appendChild(doc.createTextNode(indent))
+    if not find_child_with_attribute(application, 'meta-data', android_ns,
+                                     'name', logging_parent_key):
+      ul = doc.createElement('meta-data')
+      ul.setAttributeNS(android_ns, 'android:name', logging_parent_key)
+      ul.setAttributeNS(android_ns, 'android:value', logging_parent_value)
+      application.insertBefore(doc.createTextNode(indent), last)
+      application.insertBefore(ul, last)
+      last = application.lastChild
+
+    # align the closing tag with the opening tag if it's not
+    # indented
+    if last and last.nodeType != minidom.Node.TEXT_NODE:
+      indent = get_indent(application.previousSibling, 1)
+      application.appendChild(doc.createTextNode(indent))
 
 
 def add_uses_libraries(doc, new_uses_libraries, required):
@@ -192,42 +160,32 @@
   """
 
   manifest = parse_manifest(doc)
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
+  for application in get_or_create_applications(doc, manifest):
+    indent = get_indent(application.firstChild, 2)
 
-  indent = get_indent(application.firstChild, 2)
+    last = application.lastChild
+    if last is not None and last.nodeType != minidom.Node.TEXT_NODE:
+      last = None
 
-  last = application.lastChild
-  if last is not None and last.nodeType != minidom.Node.TEXT_NODE:
-    last = None
+    for name in new_uses_libraries:
+      if find_child_with_attribute(application, 'uses-library', android_ns,
+                                   'name', name) is not None:
+        # If the uses-library tag of the same 'name' attribute value exists,
+        # respect it.
+        continue
 
-  for name in new_uses_libraries:
-    if find_child_with_attribute(application, 'uses-library', android_ns,
-                                 'name', name) is not None:
-      # If the uses-library tag of the same 'name' attribute value exists,
-      # respect it.
-      continue
+      ul = doc.createElement('uses-library')
+      ul.setAttributeNS(android_ns, 'android:name', name)
+      ul.setAttributeNS(android_ns, 'android:required', str(required).lower())
 
-    ul = doc.createElement('uses-library')
-    ul.setAttributeNS(android_ns, 'android:name', name)
-    ul.setAttributeNS(android_ns, 'android:required', str(required).lower())
+      application.insertBefore(doc.createTextNode(indent), last)
+      application.insertBefore(ul, last)
 
-    application.insertBefore(doc.createTextNode(indent), last)
-    application.insertBefore(ul, last)
-
-  # align the closing tag with the opening tag if it's not
-  # indented
-  if application.lastChild.nodeType != minidom.Node.TEXT_NODE:
-    indent = get_indent(application.previousSibling, 1)
-    application.appendChild(doc.createTextNode(indent))
+    # align the closing tag with the opening tag if it's not
+    # indented
+    if application.lastChild.nodeType != minidom.Node.TEXT_NODE:
+      indent = get_indent(application.previousSibling, 1)
+      application.appendChild(doc.createTextNode(indent))
 
 
 def add_uses_non_sdk_api(doc):
@@ -240,112 +198,62 @@
   """
 
   manifest = parse_manifest(doc)
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
-
-  attr = application.getAttributeNodeNS(android_ns, 'usesNonSdkApi')
-  if attr is None:
-    attr = doc.createAttributeNS(android_ns, 'android:usesNonSdkApi')
-    attr.value = 'true'
-    application.setAttributeNode(attr)
+  for application in get_or_create_applications(doc, manifest):
+    attr = application.getAttributeNodeNS(android_ns, 'usesNonSdkApi')
+    if attr is None:
+      attr = doc.createAttributeNS(android_ns, 'android:usesNonSdkApi')
+      attr.value = 'true'
+      application.setAttributeNode(attr)
 
 
 def add_use_embedded_dex(doc):
   manifest = parse_manifest(doc)
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
-
-  attr = application.getAttributeNodeNS(android_ns, 'useEmbeddedDex')
-  if attr is None:
-    attr = doc.createAttributeNS(android_ns, 'android:useEmbeddedDex')
-    attr.value = 'true'
-    application.setAttributeNode(attr)
-  elif attr.value != 'true':
-    raise RuntimeError('existing attribute mismatches the option of --use-embedded-dex')
+  for application in get_or_create_applications(doc, manifest):
+    attr = application.getAttributeNodeNS(android_ns, 'useEmbeddedDex')
+    if attr is None:
+      attr = doc.createAttributeNS(android_ns, 'android:useEmbeddedDex')
+      attr.value = 'true'
+      application.setAttributeNode(attr)
+    elif attr.value != 'true':
+      raise RuntimeError('existing attribute mismatches the option of --use-embedded-dex')
 
 
 def add_extract_native_libs(doc, extract_native_libs):
   manifest = parse_manifest(doc)
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
-
-  value = str(extract_native_libs).lower()
-  attr = application.getAttributeNodeNS(android_ns, 'extractNativeLibs')
-  if attr is None:
-    attr = doc.createAttributeNS(android_ns, 'android:extractNativeLibs')
-    attr.value = value
-    application.setAttributeNode(attr)
-  elif attr.value != value:
-    raise RuntimeError('existing attribute extractNativeLibs="%s" conflicts with --extract-native-libs="%s"' %
-                       (attr.value, value))
+  for application in get_or_create_applications(doc, manifest):
+    value = str(extract_native_libs).lower()
+    attr = application.getAttributeNodeNS(android_ns, 'extractNativeLibs')
+    if attr is None:
+      attr = doc.createAttributeNS(android_ns, 'android:extractNativeLibs')
+      attr.value = value
+      application.setAttributeNode(attr)
+    elif attr.value != value:
+      raise RuntimeError('existing attribute extractNativeLibs="%s" conflicts with --extract-native-libs="%s"' %
+                         (attr.value, value))
 
 
 def set_has_code_to_false(doc):
   manifest = parse_manifest(doc)
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
-
-  attr = application.getAttributeNodeNS(android_ns, 'hasCode')
-  if attr is not None:
-    # Do nothing if the application already has a hasCode attribute.
-    return
-  attr = doc.createAttributeNS(android_ns, 'android:hasCode')
-  attr.value = 'false'
-  application.setAttributeNode(attr)
+  for application in get_or_create_applications(doc, manifest):
+    attr = application.getAttributeNodeNS(android_ns, 'hasCode')
+    if attr is not None:
+      # Do nothing if the application already has a hasCode attribute.
+      continue
+    attr = doc.createAttributeNS(android_ns, 'android:hasCode')
+    attr.value = 'false'
+    application.setAttributeNode(attr)
 
 
 def set_test_only_flag_to_true(doc):
   manifest = parse_manifest(doc)
-  elems = get_children_with_tag(manifest, 'application')
-  application = elems[0] if len(elems) == 1 else None
-  if len(elems) > 1:
-    raise RuntimeError('found multiple <application> tags')
-  elif not elems:
-    application = doc.createElement('application')
-    indent = get_indent(manifest.firstChild, 1)
-    first = manifest.firstChild
-    manifest.insertBefore(doc.createTextNode(indent), first)
-    manifest.insertBefore(application, first)
-
-  attr = application.getAttributeNodeNS(android_ns, 'testOnly')
-  if attr is not None:
-    # Do nothing If the application already has a testOnly attribute.
-    return
-  attr = doc.createAttributeNS(android_ns, 'android:testOnly')
-  attr.value = 'true'
-  application.setAttributeNode(attr)
+  for application in get_or_create_applications(doc, manifest):
+    attr = application.getAttributeNodeNS(android_ns, 'testOnly')
+    if attr is not None:
+      # Do nothing If the application already has a testOnly attribute.
+      continue
+    attr = doc.createAttributeNS(android_ns, 'android:testOnly')
+    attr.value = 'true'
+    application.setAttributeNode(attr)
 
 
 def set_max_sdk_version(doc, max_sdk_version):
diff --git a/scripts/manifest_fixer_test.py b/scripts/manifest_fixer_test.py
index 24828c7..e4d8dc3 100755
--- a/scripts/manifest_fixer_test.py
+++ b/scripts/manifest_fixer_test.py
@@ -228,6 +228,18 @@
 
     self.assert_xml_equal(output, expected)
 
+  def test_multiple_uses_sdks(self):
+    """Tests a manifest that contains multiple uses_sdks elements."""
+
+    manifest_input = self.manifest_tmpl % (
+        '    <uses-sdk android:featureFlag="foo" android:minSdkVersion="21" />\n'
+        '    <uses-sdk android:featureFlag="!foo" android:minSdkVersion="22" />\n')
+    expected = self.manifest_tmpl % (
+      '    <uses-sdk android:featureFlag="foo" android:minSdkVersion="28" android:targetSdkVersion="28" />\n'
+      '    <uses-sdk android:featureFlag="!foo" android:minSdkVersion="28" android:targetSdkVersion="28" />\n')
+
+    output = self.raise_min_sdk_version_test(manifest_input, '28', '28', False)
+    self.assert_xml_equal(output, expected)
 
 class AddLoggingParentTest(unittest.TestCase):
   """Unit tests for add_logging_parent function."""
@@ -289,18 +301,16 @@
   manifest_tmpl = (
       '<?xml version="1.0" encoding="utf-8"?>\n'
       '<manifest xmlns:android="http://schemas.android.com/apk/res/android">\n'
-      '    <application>\n'
       '%s'
-      '    </application>\n'
       '</manifest>\n')
 
   def uses_libraries(self, name_required_pairs):
-    ret = ''
+    ret = '    <application>\n'
     for name, required in name_required_pairs:
       ret += (
           '        <uses-library android:name="%s" android:required="%s"/>\n'
       ) % (name, required)
-
+    ret += '    </application>\n'
     return ret
 
   def test_empty(self):
@@ -361,6 +371,17 @@
     output = self.run_test(manifest_input, ['foo', 'bar'])
     self.assert_xml_equal(output, expected)
 
+  def test_multiple_application(self):
+    """When there are multiple applications, the libs are added to each."""
+    manifest_input = self.manifest_tmpl % (
+            self.uses_libraries([('foo', 'false')]) +
+            self.uses_libraries([('bar', 'false')]))
+    expected = self.manifest_tmpl % (
+            self.uses_libraries([('foo', 'false'), ('bar', 'true')]) +
+            self.uses_libraries([('bar', 'false'), ('foo', 'true')]))
+    output = self.run_test(manifest_input, ['foo', 'bar'])
+    self.assert_xml_equal(output, expected)
+
 
 class AddUsesNonSdkApiTest(unittest.TestCase):
   """Unit tests for add_uses_libraries function."""
@@ -378,11 +399,11 @@
   manifest_tmpl = (
       '<?xml version="1.0" encoding="utf-8"?>\n'
       '<manifest xmlns:android="http://schemas.android.com/apk/res/android">\n'
-      '    <application%s/>\n'
+      '    %s\n'
       '</manifest>\n')
 
   def uses_non_sdk_api(self, value):
-    return ' android:usesNonSdkApi="true"' if value else ''
+    return '<application %s/>' % ('android:usesNonSdkApi="true"' if value else '')
 
   def test_set_true(self):
     """Empty new_uses_libraries must not touch the manifest."""
@@ -398,6 +419,13 @@
     output = self.run_test(manifest_input)
     self.assert_xml_equal(output, expected)
 
+  def test_multiple_applications(self):
+    """new_uses_libraries must be added to all applications."""
+    manifest_input = self.manifest_tmpl % (self.uses_non_sdk_api(True) +  self.uses_non_sdk_api(False))
+    expected = self.manifest_tmpl % (self.uses_non_sdk_api(True) +  self.uses_non_sdk_api(True))
+    output = self.run_test(manifest_input)
+    self.assert_xml_equal(output, expected)
+
 
 class UseEmbeddedDexTest(unittest.TestCase):
   """Unit tests for add_use_embedded_dex function."""
@@ -415,14 +443,14 @@
   manifest_tmpl = (
       '<?xml version="1.0" encoding="utf-8"?>\n'
       '<manifest xmlns:android="http://schemas.android.com/apk/res/android">\n'
-      '    <application%s/>\n'
+      '    %s\n'
       '</manifest>\n')
 
   def use_embedded_dex(self, value):
-    return ' android:useEmbeddedDex="%s"' % value
+    return '<application android:useEmbeddedDex="%s" />' % value
 
   def test_manifest_with_undeclared_preference(self):
-    manifest_input = self.manifest_tmpl % ''
+    manifest_input = self.manifest_tmpl % '<application/>'
     expected = self.manifest_tmpl % self.use_embedded_dex('true')
     output = self.run_test(manifest_input)
     self.assert_xml_equal(output, expected)
@@ -437,6 +465,18 @@
     manifest_input = self.manifest_tmpl % self.use_embedded_dex('false')
     self.assertRaises(RuntimeError, self.run_test, manifest_input)
 
+  def test_multiple_applications(self):
+    manifest_input = self.manifest_tmpl % (
+        self.use_embedded_dex('true') +
+        '<application/>'
+    )
+    expected = self.manifest_tmpl % (
+        self.use_embedded_dex('true') +
+        self.use_embedded_dex('true')
+    )
+    output = self.run_test(manifest_input)
+    self.assert_xml_equal(output, expected)
+
 
 class AddExtractNativeLibsTest(unittest.TestCase):
   """Unit tests for add_extract_native_libs function."""
@@ -454,20 +494,20 @@
   manifest_tmpl = (
       '<?xml version="1.0" encoding="utf-8"?>\n'
       '<manifest xmlns:android="http://schemas.android.com/apk/res/android">\n'
-      '    <application%s/>\n'
+      '    %s\n'
       '</manifest>\n')
 
   def extract_native_libs(self, value):
-    return ' android:extractNativeLibs="%s"' % value
+    return '<application android:extractNativeLibs="%s" />' % value
 
   def test_set_true(self):
-    manifest_input = self.manifest_tmpl % ''
+    manifest_input = self.manifest_tmpl % '<application/>'
     expected = self.manifest_tmpl % self.extract_native_libs('true')
     output = self.run_test(manifest_input, True)
     self.assert_xml_equal(output, expected)
 
   def test_set_false(self):
-    manifest_input = self.manifest_tmpl % ''
+    manifest_input = self.manifest_tmpl % '<application/>'
     expected = self.manifest_tmpl % self.extract_native_libs('false')
     output = self.run_test(manifest_input, False)
     self.assert_xml_equal(output, expected)
@@ -482,6 +522,12 @@
     manifest_input = self.manifest_tmpl % self.extract_native_libs('true')
     self.assertRaises(RuntimeError, self.run_test, manifest_input, False)
 
+  def test_multiple_applications(self):
+    manifest_input = self.manifest_tmpl % (self.extract_native_libs('true') + '<application/>')
+    expected = self.manifest_tmpl % (self.extract_native_libs('true') + self.extract_native_libs('true'))
+    output = self.run_test(manifest_input, True)
+    self.assert_xml_equal(output, expected)
+
 
 class AddNoCodeApplicationTest(unittest.TestCase):
   """Unit tests for set_has_code_to_false function."""
@@ -527,6 +573,19 @@
     output = self.run_test(manifest_input)
     self.assert_xml_equal(output, manifest_input)
 
+  def test_multiple_applications(self):
+    """ Apply to all applications  """
+    manifest_input = self.manifest_tmpl % (
+        '    <application android:hasCode="true" />\n' +
+        '    <application android:hasCode="false" />\n' +
+        '    <application/>\n')
+    expected = self.manifest_tmpl % (
+        '    <application android:hasCode="true" />\n' +
+        '    <application android:hasCode="false" />\n' +
+        '    <application android:hasCode="false" />\n')
+    output = self.run_test(manifest_input)
+    self.assert_xml_equal(output, expected)
+
 
 class AddTestOnlyApplicationTest(unittest.TestCase):
   """Unit tests for set_test_only_flag_to_true function."""
@@ -571,6 +630,20 @@
     output = self.run_test(manifest_input)
     self.assert_xml_equal(output, manifest_input)
 
+  def test_multiple_applications(self):
+    manifest_input = self.manifest_tmpl % (
+        '    <application android:testOnly="true" />\n' +
+        '    <application android:testOnly="false" />\n' +
+        '    <application/>\n'
+    )
+    expected = self.manifest_tmpl % (
+        '    <application android:testOnly="true" />\n' +
+        '    <application android:testOnly="false" />\n' +
+        '    <application android:testOnly="true" />\n'
+    )
+    output = self.run_test(manifest_input)
+    self.assert_xml_equal(output, expected)
+
 
 class SetMaxSdkVersionTest(unittest.TestCase):
   """Unit tests for set_max_sdk_version function."""