diff --git a/java/boot_jars.go b/java/boot_jars.go
index 823275b..ac8107b 100644
--- a/java/boot_jars.go
+++ b/java/boot_jars.go
@@ -49,14 +49,36 @@
 	return true
 }
 
+// isActiveModule returns true if the given module should be considered for boot
+// jars, i.e. if it's enabled and the preferred one in case of source and
+// prebuilt alternatives.
+func isActiveModule(module android.Module) bool {
+	if !module.Enabled() {
+		return false
+	}
+	if module.IsReplacedByPrebuilt() {
+		// A source module that has been replaced by a prebuilt counterpart.
+		return false
+	}
+	if prebuilt, ok := module.(android.PrebuiltInterface); ok {
+		if p := prebuilt.Prebuilt(); p != nil {
+			return p.UsePrebuilt()
+		}
+	}
+	return true
+}
+
 func (b *bootJarsSingleton) GenerateBuildActions(ctx android.SingletonContext) {
 	config := ctx.Config()
 	if config.SkipBootJarsCheck() {
 		return
 	}
 
-	// Populate a map from module name to APEX from the boot jars. If there is a problem
-	// such as duplicate modules then fail and return immediately.
+	// Populate a map from module name to APEX from the boot jars. If there is a
+	// problem such as duplicate modules then fail and return immediately. Note
+	// that both module and APEX names are tracked by base names here, so we need
+	// to be careful to remove "prebuilt_" prefixes when comparing them with
+	// actual modules and APEX bundles.
 	moduleToApex := make(map[string]string)
 	if !populateMapFromConfiguredJarList(ctx, moduleToApex, config.NonUpdatableBootJars(), "BootJars") ||
 		!populateMapFromConfiguredJarList(ctx, moduleToApex, config.UpdatableBootJars(), "UpdatableBootJars") {
@@ -69,10 +91,14 @@
 	// Scan all the modules looking for the module/apex variants corresponding to the
 	// boot jars.
 	ctx.VisitAllModules(func(module android.Module) {
-		name := ctx.ModuleName(module)
+		if !isActiveModule(module) {
+			return
+		}
+
+		name := android.RemoveOptionalPrebuiltPrefix(ctx.ModuleName(module))
 		if apex, ok := moduleToApex[name]; ok {
 			apexInfo := ctx.ModuleProvider(module, android.ApexInfoProvider).(android.ApexInfo)
-			if (apex == "platform" && apexInfo.IsForPlatform()) || apexInfo.InApex(apex) {
+			if (apex == "platform" && apexInfo.IsForPlatform()) || apexInfo.InApexByBaseName(apex) {
 				// The module name/apex variant should be unique in the system but double check
 				// just in case something has gone wrong.
 				if existing, ok := nameToApexVariant[name]; ok {
diff --git a/java/dexpreopt_bootjars.go b/java/dexpreopt_bootjars.go
index 004cbbb..2dcc9e2 100644
--- a/java/dexpreopt_bootjars.go
+++ b/java/dexpreopt_bootjars.go
@@ -479,7 +479,7 @@
 			// A platform variant is required but this is for an apex so ignore it.
 			return -1, nil
 		}
-	} else if !android.InList(requiredApex, apexInfo.InApexes) {
+	} else if !apexInfo.InApexByBaseName(requiredApex) {
 		// An apex variant for a specific apex is required but this is the wrong apex.
 		return -1, nil
 	}
@@ -489,7 +489,7 @@
 
 	switch image.name {
 	case artBootImageName:
-		if len(apexInfo.InApexes) > 0 && allHavePrefix(apexInfo.InApexes, "com.android.art") {
+		if apexInfo.InApexByBaseName("com.android.art") || apexInfo.InApexByBaseName("com.android.art.debug") || apexInfo.InApexByBaseName("com.android.art,testing") {
 			// ok: found the jar in the ART apex
 		} else if name == "jacocoagent" && ctx.Config().IsEnvTrue("EMMA_INSTRUMENT_FRAMEWORK") {
 			// exception (skip and continue): Jacoco platform variant for a coverage build
@@ -516,21 +516,17 @@
 	return index, jar.DexJarBuildPath()
 }
 
-func allHavePrefix(list []string, prefix string) bool {
-	for _, s := range list {
-		if s != prefix && !strings.HasPrefix(s, prefix+".") {
-			return false
-		}
-	}
-	return true
-}
-
 // buildBootImage takes a bootImageConfig, creates rules to build it, and returns the image.
 func buildBootImage(ctx android.SingletonContext, image *bootImageConfig) *bootImageConfig {
 	// Collect dex jar paths for the boot image modules.
 	// This logic is tested in the apex package to avoid import cycle apex <-> java.
 	bootDexJars := make(android.Paths, image.modules.Len())
+
 	ctx.VisitAllModules(func(module android.Module) {
+		if !isActiveModule(module) {
+			return
+		}
+
 		if i, j := getBootImageJar(ctx, image, module); i != -1 {
 			if existing := bootDexJars[i]; existing != nil {
 				ctx.Errorf("Multiple dex jars found for %s:%s - %s and %s",
@@ -860,6 +856,9 @@
 		// Collect `permitted_packages` for updatable boot jars.
 		var updatablePackages []string
 		ctx.VisitAllModules(func(module android.Module) {
+			if !isActiveModule(module) {
+				return
+			}
 			if j, ok := module.(PermittedPackagesForUpdatableBootJars); ok {
 				name := ctx.ModuleName(module)
 				if i := android.IndexList(name, updatableModules); i != -1 {