diff --git a/src/test/groovy/net/fabricmc/loom/test/integration/AnnotationsApplyTest.groovy b/src/test/groovy/net/fabricmc/loom/test/integration/AnnotationsApplyTest.groovy
new file mode 100644
index 00000000..e208b378
--- /dev/null
+++ b/src/test/groovy/net/fabricmc/loom/test/integration/AnnotationsApplyTest.groovy
@@ -0,0 +1,75 @@
+/*
+ * This file is part of fabric-loom, licensed under the MIT License (MIT).
+ *
+ * Copyright (c) 2025 FabricMC
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package net.fabricmc.loom.test.integration
+
+import java.util.function.Predicate
+
+import org.objectweb.asm.ClassReader
+import org.objectweb.asm.tree.ClassNode
+import org.objectweb.asm.tree.MethodNode
+import spock.lang.Specification
+import spock.lang.Unroll
+
+import net.fabricmc.loom.test.util.GradleProjectTestTrait
+import net.fabricmc.loom.util.ZipUtils
+
+import static net.fabricmc.loom.test.LoomTestConstants.STANDARD_TEST_VERSIONS
+import static org.gradle.testkit.runner.TaskOutcome.SUCCESS
+
+class AnnotationsApplyTest extends Specification implements GradleProjectTestTrait {
+	@Unroll
+	def "annotations apply (gradle #version)"() {
+		setup:
+		def gradle = gradleProject(project: "annotationsApply", version: version)
+
+		when:
+		def result = gradle.run(task: "build")
+
+		then:
+		result.task(":build").outcome == SUCCESS
+		checkClass(gradle, "net/minecraft/util/math/BlockPos") {
+			MethodNode method = it.methods.find {
+				it.name == "add" && it.desc == "(Lnet/minecraft/util/math/Vec3i;)Lnet/minecraft/util/math/BlockPos;"
+			}
+
+			if (method == null || method.invisibleAnnotations == null) {
+				return false
+			}
+
+			method.invisibleAnnotations.any { it.desc == "Lorg/jetbrains/annotations/Contract;" }
+		}
+
+		where:
+		version << STANDARD_TEST_VERSIONS
+	}
+
+	boolean checkClass(GradleProject gradle, String clazz, Predicate<ClassNode> test) {
+		byte[] bytecode = ZipUtils.unpack(gradle.getGeneratedMinecraft("25w42a-net.fabricmc.yarn.25w42a.25w42a+build.9-v2").toPath(), "${clazz}.class")
+		ClassReader reader = new ClassReader(bytecode)
+		ClassNode node = new ClassNode()
+		reader.accept(node, 0)
+		return test.test(node)
+	}
+}
diff --git a/src/test/groovy/net/fabricmc/loom/test/util/GradleProjectTestTrait.groovy b/src/test/groovy/net/fabricmc/loom/test/util/GradleProjectTestTrait.groovy
index d14673be..86df3a47 100644
--- a/src/test/groovy/net/fabricmc/loom/test/util/GradleProjectTestTrait.groovy
+++ b/src/test/groovy/net/fabricmc/loom/test/util/GradleProjectTestTrait.groovy
@@ -24,7 +24,6 @@
 
 package net.fabricmc.loom.test.util
 
-import groovy.io.FileType
 import groovy.transform.Immutable
 import org.apache.commons.io.FileUtils
 import org.gradle.testkit.runner.BuildResult
@@ -261,25 +260,33 @@ trait GradleProjectTestTrait {
 			return ZipUtils.unpackNullable(file.toPath(), entryName) != null
 		}
 
-		File getGeneratedSources(String mappings, String jarType = "merged") {
-			return new File(getGradleHomeDir(), "caches/fabric-loom/minecraftMaven/net/minecraft/minecraft-${jarType}/${mappings}/minecraft-${jarType}-${mappings}-sources.jar")
+		File getGeneratedMinecraft(String mappings, String jarType = "merged", String classifier = "") {
+			String classifierSuffix = classifier.isEmpty() ? "" : "-$classifier"
+			return new File(getGradleHomeDir(), "caches/fabric-loom/minecraftMaven/net/minecraft/minecraft-${jarType}/${mappings}/minecraft-${jarType}-${mappings}${classifierSuffix}.jar")
 		}
 
-		File getGeneratedLocalSources(String mappings) {
-			File file
-			getProjectDir().traverse(type: FileType.FILES) {
-				if (it.name.startsWith("minecraft-merged-")
-						&& it.name.contains(mappings)
-						&& it.name.endsWith("-sources.jar")) {
-					file = it
-				}
+		File getGeneratedSources(String mappings, String jarType = "merged") {
+			return getGeneratedMinecraft(mappings, jarType, "sources")
+		}
+
+		File getGeneratedLocalMinecraft(String mappings, String jarType = "merged", String classifier = "") {
+			String classifierSuffix = classifier.isEmpty() ? "" : "-$classifier"
+
+			File file = new File(getProjectDir(), ".gradle/loom-cache/minecraftMaven/net/minecraft")
+			file = file.listFiles().find {
+				it.name.startsWith("minecraft-${jarType}-")
 			}
 
 			if (file == null) {
 				throw new FileNotFoundException()
 			}
 
-			return file
+			String jarFileName = "${file.name}-${mappings}${classifierSuffix}.jar"
+			return new File(file, "${mappings}/${jarFileName}")
+		}
+
+		File getGeneratedLocalSources(String mappings, String jarType = "merged") {
+			return getGeneratedLocalMinecraft(mappings, jarType, "sources")
 		}
 
 		void buildSrc(String name, boolean apply = true) {
diff --git a/src/test/resources/projects/annotationsApply/build.gradle b/src/test/resources/projects/annotationsApply/build.gradle
new file mode 100644
index 00000000..7aec635b
--- /dev/null
+++ b/src/test/resources/projects/annotationsApply/build.gradle
@@ -0,0 +1,9 @@
+plugins {
+	id 'fabric-loom'
+}
+
+dependencies {
+	minecraft "com.mojang:minecraft:25w42a"
+	mappings "net.fabricmc:yarn:25w42a+build.9:v2"
+	modImplementation "net.fabricmc:fabric-loader:0.17.3"
+}
diff --git a/src/test/resources/projects/annotationsApply/src/main/java/ExampleMod.java b/src/test/resources/projects/annotationsApply/src/main/java/ExampleMod.java
new file mode 100644
index 00000000..f6675524
--- /dev/null
+++ b/src/test/resources/projects/annotationsApply/src/main/java/ExampleMod.java
@@ -0,0 +1,8 @@
+
+import net.fabricmc.api.ModInitializer;
+
+public class ExampleMod implements ModInitializer {
+	@Override
+	public void onInitialize() {
+	}
+}