diff --git a/apex/apex_test.go b/apex/apex_test.go
index 983b820..88da21b 100644
--- a/apex/apex_test.go
+++ b/apex/apex_test.go
@@ -4639,11 +4639,13 @@
 		}
 	}
 
-	checkHiddenAPIIndexInputs := func(t *testing.T, ctx *android.TestContext, expectedInputs string) {
+	checkHiddenAPIIndexInputs := func(t *testing.T, ctx *android.TestContext, expectedIntermediateInputs string) {
 		t.Helper()
 		platformBootclasspath := ctx.ModuleForTests("platform-bootclasspath", "android_common")
-		indexRule := platformBootclasspath.Rule("monolithic_hidden_API_index")
-		java.CheckHiddenAPIRuleInputs(t, "index", expectedInputs, indexRule)
+		var rule android.TestingBuildParams
+
+		rule = platformBootclasspath.Output("hiddenapi-monolithic/index-from-classes.csv")
+		java.CheckHiddenAPIRuleInputs(t, "intermediate index", expectedIntermediateInputs, rule)
 	}
 
 	fragment := java.ApexVariantReference{
diff --git a/java/hiddenapi_modular.go b/java/hiddenapi_modular.go
index de72b39..6e22614 100644
--- a/java/hiddenapi_modular.go
+++ b/java/hiddenapi_modular.go
@@ -524,7 +524,7 @@
 		}
 	}
 
-	ctx.VisitDirectDepsIf(isActiveModule, func(module android.Module) {
+	ctx.VisitDirectDeps(func(module android.Module) {
 		tag := ctx.OtherModuleDependencyTag(module)
 		if hiddenAPIStubsTag, ok := tag.(hiddenAPIStubsDependencyTag); ok {
 			kind := hiddenAPIStubsTag.sdkKind
@@ -634,7 +634,7 @@
 // hiddenAPIInfo is a struct containing paths to files that augment the information provided by
 // the annotationFlags.
 func buildRuleToGenerateHiddenApiFlags(ctx android.BuilderContext, name, desc string,
-	outputPath android.WritablePath, baseFlagsPath android.Path, annotationFlags android.Path,
+	outputPath android.WritablePath, baseFlagsPath android.Path, annotationFlagPaths android.Paths,
 	flagFilesByCategory FlagFilesByCategory, allFlagsPaths android.Paths, generatedRemovedDexSignatures android.OptionalPath) {
 
 	// The file which is used to record that the flags file is valid.
@@ -665,7 +665,7 @@
 	command := rule.Command().
 		BuiltTool("generate_hiddenapi_lists").
 		FlagWithInput("--csv ", baseFlagsPath).
-		Input(annotationFlags).
+		Inputs(annotationFlagPaths).
 		FlagWithOutput("--output ", tempPath)
 
 	// Add the options for the different categories of flag files.
@@ -747,7 +747,7 @@
 	// Generate the all-flags.csv which are the flags that will, in future, be encoded into the dex
 	// files.
 	allFlagsCSV := android.PathForModuleOut(ctx, hiddenApiSubDir, "all-flags.csv")
-	buildRuleToGenerateHiddenApiFlags(ctx, "modularHiddenApiAllFlags", "modular hiddenapi all flags", allFlagsCSV, stubFlagsCSV, annotationFlagsCSV, input.FlagFilesByCategory, nil, removedDexSignatures)
+	buildRuleToGenerateHiddenApiFlags(ctx, "modularHiddenApiAllFlags", "modular hiddenapi all flags", allFlagsCSV, stubFlagsCSV, android.Paths{annotationFlagsCSV}, input.FlagFilesByCategory, nil, removedDexSignatures)
 
 	// Encode the flags into the boot dex files.
 	encodedBootDexJarsByModule := map[string]android.Path{}
diff --git a/java/hiddenapi_monolithic.go b/java/hiddenapi_monolithic.go
index 8a83d10..52f0770 100644
--- a/java/hiddenapi_monolithic.go
+++ b/java/hiddenapi_monolithic.go
@@ -68,6 +68,14 @@
 			if ctx.OtherModuleHasProvider(fragment, HiddenAPIInfoProvider) {
 				info := ctx.OtherModuleProvider(fragment, HiddenAPIInfoProvider).(HiddenAPIInfo)
 				monolithicInfo.append(&info)
+
+				// If the bootclasspath fragment actually perform hidden API processing itself then use the
+				// CSV files it provides and do not bother processing the classesJars files. This ensures
+				// consistent behavior between source and prebuilt as prebuilt modules do not provide
+				// classesJars.
+				if info.AllFlagsPath != nil {
+					continue
+				}
 			}
 
 			classesJars = extractClassesJarsFromModules(e.Contents)
diff --git a/java/platform_bootclasspath.go b/java/platform_bootclasspath.go
index 3f5c940..cd00c19 100644
--- a/java/platform_bootclasspath.go
+++ b/java/platform_bootclasspath.go
@@ -302,28 +302,48 @@
 	rule.Build("platform-bootclasspath-monolithic-hiddenapi-stub-flags", "monolithic hidden API stub flags")
 
 	// Generate the annotation-flags.csv file from all the module annotations.
-	annotationFlags := android.PathForModuleOut(ctx, "hiddenapi-monolithic", "annotation-flags.csv")
-	buildRuleToGenerateAnnotationFlags(ctx, "monolithic hiddenapi flags", classesJars, stubFlags, annotationFlags)
+	annotationFlags := android.PathForModuleOut(ctx, "hiddenapi-monolithic", "annotation-flags-from-classes.csv")
+	buildRuleToGenerateAnnotationFlags(ctx, "intermediate hidden API flags", classesJars, stubFlags, annotationFlags)
 
-	// Generate the monotlithic hiddenapi-flags.csv file.
+	// Generate the monolithic hiddenapi-flags.csv file.
+	//
+	// Use annotation flags generated directly from the classes jars as well as annotation flag files
+	// provided by prebuilts.
+	allAnnotationFlagFiles := android.Paths{annotationFlags}
+	allAnnotationFlagFiles = append(allAnnotationFlagFiles, monolithicInfo.AnnotationFlagsPaths...)
 	allFlags := hiddenAPISingletonPaths(ctx).flags
-	buildRuleToGenerateHiddenApiFlags(ctx, "hiddenAPIFlagsFile", "hiddenapi flags", allFlags, stubFlags, annotationFlags, monolithicInfo.FlagsFilesByCategory, monolithicInfo.AllFlagsPaths, android.OptionalPath{})
+	buildRuleToGenerateHiddenApiFlags(ctx, "hiddenAPIFlagsFile", "monolithic hidden API flags", allFlags, stubFlags, allAnnotationFlagFiles, monolithicInfo.FlagsFilesByCategory, monolithicInfo.AllFlagsPaths, android.OptionalPath{})
 
 	// Generate an intermediate monolithic hiddenapi-metadata.csv file directly from the annotations
 	// in the source code.
-	intermediateMetadataCSV := android.PathForModuleOut(ctx, "hiddenapi-monolithic", "intermediate-metadata.csv")
-	buildRuleToGenerateMetadata(ctx, "monolithic hidden API metadata", classesJars, stubFlags, intermediateMetadataCSV)
+	intermediateMetadataCSV := android.PathForModuleOut(ctx, "hiddenapi-monolithic", "metadata-from-classes.csv")
+	buildRuleToGenerateMetadata(ctx, "intermediate hidden API metadata", classesJars, stubFlags, intermediateMetadataCSV)
 
-	// Reformat the intermediate file to add | quotes just in case that is important for the tools
-	// that consume the metadata file.
-	// TODO(b/179354495): Investigate whether it is possible to remove this reformatting step.
+	// Generate the monolithic hiddenapi-metadata.csv file.
+	//
+	// Use metadata files generated directly from the classes jars as well as metadata files provided
+	// by prebuilts.
+	//
+	// This has the side effect of ensuring that the output file uses | quotes just in case that is
+	// important for the tools that consume the metadata file.
+	allMetadataFlagFiles := android.Paths{intermediateMetadataCSV}
+	allMetadataFlagFiles = append(allMetadataFlagFiles, monolithicInfo.MetadataPaths...)
 	metadataCSV := hiddenAPISingletonPaths(ctx).metadata
-	b.buildRuleMergeCSV(ctx, "reformat monolithic hidden API metadata", android.Paths{intermediateMetadataCSV}, metadataCSV)
+	b.buildRuleMergeCSV(ctx, "monolithic hidden API metadata", allMetadataFlagFiles, metadataCSV)
 
-	// Generate the monolithic hiddenapi-index.csv file directly from the CSV files in the classes
-	// jars.
+	// Generate an intermediate monolithic hiddenapi-index.csv file directly from the CSV files in the
+	// classes jars.
+	intermediateIndexCSV := android.PathForModuleOut(ctx, "hiddenapi-monolithic", "index-from-classes.csv")
+	buildRuleToGenerateIndex(ctx, "intermediate hidden API index", classesJars, intermediateIndexCSV)
+
+	// Generate the monolithic hiddenapi-index.csv file.
+	//
+	// Use index files generated directly from the classes jars as well as index files provided
+	// by prebuilts.
+	allIndexFlagFiles := android.Paths{intermediateIndexCSV}
+	allIndexFlagFiles = append(allIndexFlagFiles, monolithicInfo.IndexPaths...)
 	indexCSV := hiddenAPISingletonPaths(ctx).index
-	buildRuleToGenerateIndex(ctx, "monolithic hidden API index", classesJars, indexCSV)
+	b.buildRuleMergeCSV(ctx, "monolithic hidden API index", allIndexFlagFiles, indexCSV)
 
 	return bootDexJarByModule
 }
diff --git a/java/platform_bootclasspath_test.go b/java/platform_bootclasspath_test.go
index 87a6411..1c2a3ae 100644
--- a/java/platform_bootclasspath_test.go
+++ b/java/platform_bootclasspath_test.go
@@ -318,10 +318,41 @@
 	// Make sure that the foo-hiddenapi-annotations.jar is included in the inputs to the rules that
 	// creates the index.csv file.
 	platformBootclasspath := result.ModuleForTests("myplatform-bootclasspath", "android_common")
-	indexRule := platformBootclasspath.Rule("monolithic_hidden_API_index")
-	CheckHiddenAPIRuleInputs(t, "index", `
-			out/soong/.intermediates/bar/android_common/javac/bar.jar
-			out/soong/.intermediates/foo-hiddenapi-annotations/android_common/javac/foo-hiddenapi-annotations.jar
-			out/soong/.intermediates/foo/android_common/javac/foo.jar
-	`, indexRule)
+
+	var rule android.TestingBuildParams
+
+	// All the intermediate rules use the same inputs.
+	expectedIntermediateInputs := `
+		out/soong/.intermediates/bar/android_common/javac/bar.jar
+		out/soong/.intermediates/foo-hiddenapi-annotations/android_common/javac/foo-hiddenapi-annotations.jar
+		out/soong/.intermediates/foo/android_common/javac/foo.jar
+	`
+
+	// Check flags output.
+	rule = platformBootclasspath.Output("hiddenapi-monolithic/annotation-flags-from-classes.csv")
+	CheckHiddenAPIRuleInputs(t, "intermediate flags", expectedIntermediateInputs, rule)
+
+	rule = platformBootclasspath.Output("out/soong/hiddenapi/hiddenapi-flags.csv")
+	CheckHiddenAPIRuleInputs(t, "monolithic flags", `
+		out/soong/.intermediates/myplatform-bootclasspath/android_common/hiddenapi-monolithic/annotation-flags-from-classes.csv
+		out/soong/hiddenapi/hiddenapi-stub-flags.txt
+	`, rule)
+
+	// Check metadata output.
+	rule = platformBootclasspath.Output("hiddenapi-monolithic/metadata-from-classes.csv")
+	CheckHiddenAPIRuleInputs(t, "intermediate metadata", expectedIntermediateInputs, rule)
+
+	rule = platformBootclasspath.Output("out/soong/hiddenapi/hiddenapi-unsupported.csv")
+	CheckHiddenAPIRuleInputs(t, "monolithic metadata", `
+		out/soong/.intermediates/myplatform-bootclasspath/android_common/hiddenapi-monolithic/metadata-from-classes.csv
+	`, rule)
+
+	// Check index output.
+	rule = platformBootclasspath.Output("hiddenapi-monolithic/index-from-classes.csv")
+	CheckHiddenAPIRuleInputs(t, "intermediate index", expectedIntermediateInputs, rule)
+
+	rule = platformBootclasspath.Output("out/soong/hiddenapi/hiddenapi-index.csv")
+	CheckHiddenAPIRuleInputs(t, "monolithic index", `
+		out/soong/.intermediates/myplatform-bootclasspath/android_common/hiddenapi-monolithic/index-from-classes.csv
+	`, rule)
 }
diff --git a/sdk/bootclasspath_fragment_sdk_test.go b/sdk/bootclasspath_fragment_sdk_test.go
index 1f28ed3..378f7cf 100644
--- a/sdk/bootclasspath_fragment_sdk_test.go
+++ b/sdk/bootclasspath_fragment_sdk_test.go
@@ -484,6 +484,28 @@
 .intermediates/mycoreplatform.stubs.source/android_common/metalava/mycoreplatform.stubs.source_removed.txt -> sdk_library/public/mycoreplatform-removed.txt
 `),
 		snapshotTestPreparer(checkSnapshotWithoutSource, preparerForSnapshot),
+		snapshotTestChecker(checkSnapshotWithoutSource, func(t *testing.T, result *android.TestResult) {
+			module := result.ModuleForTests("platform-bootclasspath", "android_common")
+			var rule android.TestingBuildParams
+			rule = module.Output("out/soong/hiddenapi/hiddenapi-flags.csv")
+			java.CheckHiddenAPIRuleInputs(t, "monolithic flags", `
+				out/soong/.intermediates/frameworks/base/boot/platform-bootclasspath/android_common/hiddenapi-monolithic/annotation-flags-from-classes.csv
+        out/soong/hiddenapi/hiddenapi-stub-flags.txt
+        snapshot/hiddenapi/annotation-flags.csv
+			`, rule)
+
+			rule = module.Output("out/soong/hiddenapi/hiddenapi-unsupported.csv")
+			java.CheckHiddenAPIRuleInputs(t, "monolithic metadata", `
+				out/soong/.intermediates/frameworks/base/boot/platform-bootclasspath/android_common/hiddenapi-monolithic/metadata-from-classes.csv
+        snapshot/hiddenapi/metadata.csv
+			`, rule)
+
+			rule = module.Output("out/soong/hiddenapi/hiddenapi-index.csv")
+			java.CheckHiddenAPIRuleInputs(t, "monolithic index", `
+				out/soong/.intermediates/frameworks/base/boot/platform-bootclasspath/android_common/hiddenapi-monolithic/index-from-classes.csv
+        snapshot/hiddenapi/index.csv
+			`, rule)
+		}),
 		snapshotTestPreparer(checkSnapshotWithSourcePreferred, preparerForSnapshot),
 		snapshotTestPreparer(checkSnapshotPreferredWithSource, preparerForSnapshot),
 	)