diff --git a/java/base.go b/java/base.go
index ef299b2..3d42f46 100644
--- a/java/base.go
+++ b/java/base.go
@@ -1735,8 +1735,12 @@
 		return
 	}
 
+	completeStaticLibsImplementationJarsToCombine := completeStaticLibsImplementationJars
+
 	if j.shouldInstrument(ctx) {
-		outputFile = j.instrument(ctx, flags, outputFile, jarName, specs)
+		instrumentedOutputFile := j.instrument(ctx, flags, outputFile, jarName, specs)
+		completeStaticLibsImplementationJarsToCombine = android.NewDepSet(android.PREORDER, android.Paths{instrumentedOutputFile}, nil)
+		outputFile = instrumentedOutputFile
 	}
 
 	// merge implementation jar with resources if necessary
@@ -1744,7 +1748,7 @@
 	if ctx.Config().UseTransitiveJarsInClasspath() {
 		resourceJars := completeStaticLibsResourceJars.ToList()
 		if len(resourceJars) > 0 {
-			implementationAndResourcesJarsToCombine = append(resourceJars, completeStaticLibsImplementationJars.ToList()...)
+			implementationAndResourcesJarsToCombine = append(resourceJars, completeStaticLibsImplementationJarsToCombine.ToList()...)
 			implementationAndResourcesJarsToCombine = append(implementationAndResourcesJarsToCombine, extraDepCombinedJars...)
 		}
 	} else {
diff --git a/java/java_test.go b/java/java_test.go
index c13db3e..dbbf4a8 100644
--- a/java/java_test.go
+++ b/java/java_test.go
@@ -3065,6 +3065,43 @@
 		"baz.jar", bazOutputPaths[0].Rel())
 }
 
+func TestCoverage(t *testing.T) {
+	result := android.GroupFixturePreparers(
+		PrepareForTestWithJavaDefaultModules,
+		prepareForTestWithFrameworkJacocoInstrumentation,
+		PrepareForTestWithTransitiveClasspathEnabled,
+	).RunTestWithBp(t, `
+		android_app {
+			name: "foo",
+			srcs: ["foo.java"],
+			static_libs: ["android.car"],
+			platform_apis: true,
+		}
+
+		// A library in InstrumentFrameworkModules
+		java_library {
+			name: "android.car",
+			srcs: ["android.car.java"],
+		}
+	`)
+
+	foo := result.ModuleForTests("foo", "android_common")
+	androidCar := result.ModuleForTests("android.car", "android_common")
+
+	fooJacoco := foo.Rule("jacoco")
+	fooCombine := foo.Description("for javac")
+
+	androidCarJacoco := androidCar.Rule("jacoco")
+	androidCarJavac := androidCar.Rule("javac")
+
+	android.AssertStringEquals(t, "foo instrumentation rule inputs", fooJacoco.Input.String(), fooCombine.Output.String())
+	android.AssertStringEquals(t, "android.car instrumentation rule inputs", androidCarJacoco.Input.String(), androidCarJavac.Output.String())
+
+	// The input to instrumentation for the `foo` app contains the non-instrumented android.car classes.
+	android.AssertStringListContains(t, "foo combined inputs", fooCombine.Inputs.Strings(), androidCarJavac.Output.String())
+	android.AssertStringListDoesNotContain(t, "foo combined inputs", fooCombine.Inputs.Strings(), androidCarJacoco.Output.String())
+}
+
 func assertTestOnlyAndTopLevel(t *testing.T, ctx *android.TestResult, expectedTestOnly []string, expectedTopLevel []string) {
 	t.Helper()
 	actualTrueModules := []string{}