diff --git a/tools/gn2bp/Android.bp.swp b/tools/gn2bp/Android.bp.swp
index 555c5d4..49813b3 100644
--- a/tools/gn2bp/Android.bp.swp
+++ b/tools/gn2bp/Android.bp.swp
@@ -1920,7 +1920,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/cert/ && $(location aprotoc) --proto_path=external/chromium_org/net/cert --cpp_out=lite=true:$(genDir)/external/chromium_org/net/cert/ $(in)",
     out: [
         "external/chromium_org/net/cert/root_store.pb.cc",
     ],
@@ -1935,7 +1935,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/cert/ && $(location aprotoc) --proto_path=external/chromium_org/net/cert --cpp_out=lite=true:$(genDir)/external/chromium_org/net/cert/ $(in)",
     out: [
         "external/chromium_org/net/cert/root_store.pb.h",
     ],
@@ -2089,7 +2089,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/base/ && $(location aprotoc) --proto_path=external/chromium_org/net/base --cpp_out=lite=true:$(genDir)/external/chromium_org/net/base/ $(in)",
     out: [
         "external/chromium_org/net/base/isolation_info.pb.cc",
     ],
@@ -2104,7 +2104,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/base/ && $(location aprotoc) --proto_path=external/chromium_org/net/base --cpp_out=lite=true:$(genDir)/external/chromium_org/net/base/ $(in)",
     out: [
         "external/chromium_org/net/base/isolation_info.pb.h",
     ],
@@ -2830,7 +2830,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/nqe/proto/ && $(location aprotoc) --proto_path=external/chromium_org/net/nqe/proto --cpp_out=lite=true:$(genDir)/external/chromium_org/net/nqe/proto/ $(in)",
     out: [
         "external/chromium_org/net/nqe/proto/network_id_proto.pb.cc",
     ],
@@ -2845,7 +2845,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/nqe/proto/ && $(location aprotoc) --proto_path=external/chromium_org/net/nqe/proto --cpp_out=lite=true:$(genDir)/external/chromium_org/net/nqe/proto/ $(in)",
     out: [
         "external/chromium_org/net/nqe/proto/network_id_proto.pb.h",
     ],
@@ -2916,7 +2916,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/third_party/quiche/src/ && $(location aprotoc) --proto_path=external/chromium_org/net/third_party/quiche/src --cpp_out=lite=true:$(genDir)/external/chromium_org/net/third_party/quiche/src/ $(in)",
     out: [
         "external/chromium_org/net/third_party/quiche/src/quiche/quic/core/proto/cached_network_parameters.pb.cc",
         "external/chromium_org/net/third_party/quiche/src/quiche/quic/core/proto/crypto_server_config.pb.cc",
@@ -2935,7 +2935,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/third_party/quiche/src/ && $(location aprotoc) --proto_path=external/chromium_org/net/third_party/quiche/src --cpp_out=lite=true:$(genDir)/external/chromium_org/net/third_party/quiche/src/ $(in)",
     out: [
         "external/chromium_org/net/third_party/quiche/src/quiche/quic/core/proto/cached_network_parameters.pb.h",
         "external/chromium_org/net/third_party/quiche/src/quiche/quic/core/proto/crypto_server_config.pb.h",
@@ -2956,7 +2956,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools/ && $(location aprotoc) --proto_path=external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools --cpp_out=lite=true:$(genDir)/external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools/ $(in)",
     out: [
         "external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools/send_algorithm_test_result.pb.cc",
     ],
@@ -2971,7 +2971,7 @@
     tools: [
         "aprotoc",
     ],
-    cmd: "mkdir -p $(genDir)/external/chromium_org/ && $(location aprotoc) --proto_path=external/chromium_org --cpp_out=lite=true:$(genDir)/external/chromium_org/ $(in)",
+    cmd: "mkdir -p $(genDir)/external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools/ && $(location aprotoc) --proto_path=external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools --cpp_out=lite=true:$(genDir)/external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools/ $(in)",
     out: [
         "external/chromium_org/net/third_party/quiche/src/quiche/quic/test_tools/send_algorithm_test_result.pb.h",
     ],
diff --git a/tools/gn2bp/gen_android_bp b/tools/gn2bp/gen_android_bp
index 7d5795a..ffb0741 100755
--- a/tools/gn2bp/gen_android_bp
+++ b/tools/gn2bp/gen_android_bp
@@ -494,13 +494,13 @@
   assert (target.type == 'proto_library')
 
   tools = {'aprotoc'}
-  cpp_out_dir = '$(genDir)/%s/' % tree_path
+  cpp_out_dir = '$(genDir)/%s/%s/' % (tree_path, target.proto_in_dir)
   target_module_name = label_to_module_name(target.name)
 
   # In GN builds the proto path is always relative to the output directory
   # (out/tmp.xxx).
   cmd = ['mkdir -p %s &&' % cpp_out_dir, '$(location aprotoc)']
-  cmd += ['--proto_path=%s' % tree_path]
+  cmd += ['--proto_path=%s/%s' % (tree_path, target.proto_in_dir)]
 
   if buildtools_protobuf_src in target.proto_paths:
     cmd += ['--proto_path=%s' % android_protobuf_src]
diff --git a/tools/gn2bp/gn_utils.py b/tools/gn2bp/gn_utils.py
index 589b12a..6fcc0f8 100644
--- a/tools/gn2bp/gn_utils.py
+++ b/tools/gn2bp/gn_utils.py
@@ -110,6 +110,7 @@
       self.proto_plugin = None
       self.proto_paths = set()
       self.proto_exports = set()
+      self.proto_in_dir = ""
 
       self.sources = set()
       # TODO(primiano): consider whether the public section should be part of
@@ -232,6 +233,7 @@
       target.proto_plugin = proto_target_type
       target.proto_paths.update(self.get_proto_paths(proto_desc))
       target.proto_exports.update(self.get_proto_exports(proto_desc))
+      target.proto_in_dir = self.get_proto_in_dir(proto_desc)
       target.sources.update(proto_desc.get('sources', []))
       assert (all(x.endswith('.proto') for x in target.sources))
     elif target.type == 'source_set':
@@ -322,6 +324,11 @@
     metadata = proto_desc.get('metadata', {})
     return metadata.get('import_dirs', [])
 
+
+  def get_proto_in_dir(self, proto_desc):
+    args = proto_desc.get('args')
+    return re.sub('^\.\./\.\./', '', args[args.index('--proto-in-dir') + 1])
+
   def get_proto_target_type(self, target):
     """ Checks if the target is a proto library and return the plugin.