diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/aot/AbstractAot.java b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/aot/AbstractAot.java
index d2dda58575..0a86342b76 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/aot/AbstractAot.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/aot/AbstractAot.java
@@ -92,7 +92,7 @@ public abstract class AbstractAot extends JavaExec {
 	@IgnoreEmptyDirectories
 	@PathSensitive(PathSensitivity.RELATIVE)
 	public final FileCollection getInputClasses() {
-		return this.inputClasses.getAsFileTree().matching((filter) -> filter.include((spec) -> !spec.isDirectory()));
+		return this.inputClasses.getAsFileTree();
 	}
 
 	public void setInputClasses(FileCollection inputClasses) {
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests.java b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests.java
index 1bf77abc19..00aa32533d 100644
--- a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests.java
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests.java
@@ -101,10 +101,35 @@ class SpringBootAotPluginIntegrationTests {
 				.isEqualTo(TaskOutcome.NO_SOURCE);
 	}
 
+	@TestTemplate
+	void processAotRunsWhenProjectHasMainSource() throws IOException {
+		writeMainClass("org.springframework.boot", "AotProcessor");
+		writeMainClass("com.example", "Main");
+		assertThat(this.gradleBuild.build("processAot").task(":processAot").getOutcome())
+				.isEqualTo(TaskOutcome.SUCCESS);
+	}
+
 	@TestTemplate
 	void processTestAotIsSkippedWhenProjectHasNoTestSource() {
 		assertThat(this.gradleBuild.build("processTestAot").task(":processTestAot").getOutcome())
 				.isEqualTo(TaskOutcome.NO_SOURCE);
 	}
 
+	private void writeMainClass(String packageName, String className) throws IOException {
+		File java = new File(this.gradleBuild.getProjectDir(),
+				"src/main/java/" + packageName.replace(".", "/") + "/" + className + ".java");
+		java.getParentFile().mkdirs();
+		Files.writeString(java.toPath(), """
+				package %s;
+
+				public class %s {
+
+					public static void main(String[] args) {
+
+					}
+
+				}
+				""".formatted(packageName, className));
+	}
+
 }
diff --git a/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests-processAotRunsWhenProjectHasMainSource.gradle b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests-processAotRunsWhenProjectHasMainSource.gradle
new file mode 100644
index 0000000000..b77b1da056
--- /dev/null
+++ b/spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/resources/org/springframework/boot/gradle/plugin/SpringBootAotPluginIntegrationTests-processAotRunsWhenProjectHasMainSource.gradle
@@ -0,0 +1,13 @@
+plugins {
+	id 'org.springframework.boot'
+	id 'org.springframework.boot.aot'
+	id 'java'
+}
+
+repositories {
+	mavenCentral()
+}
+
+springBoot {
+	mainClass = 'com.example.Main'
+}