diff --git a/src/main/java/net/fabricmc/loom/extension/MixinExtensionImpl.java b/src/main/java/net/fabricmc/loom/extension/MixinExtensionImpl.java
index c8bf56a..d79f5d6 100644
--- a/src/main/java/net/fabricmc/loom/extension/MixinExtensionImpl.java
+++ b/src/main/java/net/fabricmc/loom/extension/MixinExtensionImpl.java
@@ -76,7 +76,7 @@ public class MixinExtensionImpl extends MixinExtensionApiImpl implements MixinEx
 	protected PatternSet add0(SourceSet sourceSet, Provider<String> refmapName) {
 		if (!super.getUseLegacyMixinAp().get()) throw new IllegalStateException("You need to set useLegacyMixinAp = true to configure Mixin annotation processor.");
 
-		PatternSet pattern = new PatternSet().setIncludes(Collections.singletonList("*.json"));
+		PatternSet pattern = new PatternSet().setIncludes(Collections.singletonList("**/*.json"));
 		MixinExtension.setMixinInformationContainer(sourceSet, new MixinExtension.MixinInformationContainer(sourceSet, refmapName, pattern));
 
 		isDefault = false;
diff --git a/src/main/java/net/fabricmc/loom/task/RemapJarTask.java b/src/main/java/net/fabricmc/loom/task/RemapJarTask.java
index 16b8642..a9d357a 100644
--- a/src/main/java/net/fabricmc/loom/task/RemapJarTask.java
+++ b/src/main/java/net/fabricmc/loom/task/RemapJarTask.java
@@ -136,12 +136,34 @@ public abstract class RemapJarTask extends AbstractRemapJarTask {
 					MixinExtension.getMixinInformationContainer(sourceSet)
 			);
 
+			String[] rootPaths = sourceSet.getResources().getSrcDirs().stream()
+					.map(root -> {
+						String rootPath = root.getAbsolutePath().replace("\\", "/");
+
+						if (rootPath.charAt(rootPath.length() - 1) != '/') {
+							rootPath += '/';
+						}
+
+						return rootPath;
+					})
+					.toArray(String[]::new);
+
 			final String refmapName = container.refmapNameProvider().get();
 			final List<String> mixinConfigs = container.sourceSet().getResources()
 					.matching(container.mixinConfigPattern())
 					.getFiles()
 					.stream()
-					.map(File::getName)
+					.map(file -> {
+						String s = file.getAbsolutePath().replace("\\", "/");
+
+						for (String rootPath : rootPaths) {
+							if (s.startsWith(rootPath)) {
+								s = s.substring(rootPath.length());
+							}
+						}
+
+						return s;
+					})
 					.filter(allMixinConfigs::contains)
 					.toList();
 
diff --git a/src/test/groovy/net/fabricmc/loom/test/integration/MixinApAutoRefmapTest.groovy b/src/test/groovy/net/fabricmc/loom/test/integration/MixinApAutoRefmapTest.groovy
index f8b5b6d..69bfa93 100644
--- a/src/test/groovy/net/fabricmc/loom/test/integration/MixinApAutoRefmapTest.groovy
+++ b/src/test/groovy/net/fabricmc/loom/test/integration/MixinApAutoRefmapTest.groovy
@@ -67,6 +67,9 @@ class MixinApAutoRefmapTest extends Specification implements GradleProjectTestTr
             def j5 = JsonParser.parseReader(new InputStreamReader(jar.getInputStream(jar.getEntry("irrelevant.mixins.json"))))
             !j5.asJsonObject.has("refmap")
 
+            def j6 = JsonParser.parseReader(new InputStreamReader(jar.getInputStream(jar.getEntry("subfolder/subfolder.mixins.json"))))
+            j6.asJsonObject.getAsJsonPrimitive("refmap").getAsString() == "refmap0001.json"
+
         where:
             version << STANDARD_TEST_VERSIONS
     }
diff --git a/src/test/resources/projects/mixinApAutoRefmap/src/main/java/net/fabricmc/example/mixin/ExampleMixinSubfolder.java b/src/test/resources/projects/mixinApAutoRefmap/src/main/java/net/fabricmc/example/mixin/ExampleMixinSubfolder.java
new file mode 100644
index 0000000..519929e
--- /dev/null
+++ b/src/test/resources/projects/mixinApAutoRefmap/src/main/java/net/fabricmc/example/mixin/ExampleMixinSubfolder.java
@@ -0,0 +1,15 @@
+package net.fabricmc.example.mixin;
+
+import net.minecraft.client.gui.screen.ChatScreen;
+import org.spongepowered.asm.mixin.Mixin;
+import org.spongepowered.asm.mixin.injection.At;
+import org.spongepowered.asm.mixin.injection.Inject;
+import org.spongepowered.asm.mixin.injection.callback.CallbackInfo;
+
+@Mixin(ChatScreen.class)
+public class ExampleMixinSubfolder {
+	@Inject(at = @At("HEAD"), method = "init()V")
+	private void init(CallbackInfo info) {
+		System.out.println("This line is printed by an example mod mixin!");
+	}
+}
diff --git a/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/fabric.mod.json b/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/fabric.mod.json
index 62efe82..c92f0ce 100644
--- a/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/fabric.mod.json
+++ b/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/fabric.mod.json
@@ -24,6 +24,7 @@
   },
   "mixins": [
     "main.mixins.json",
+    "subfolder/subfolder.mixins.json",
     {
       "config": "blabla.json",
       "environment": "client"
diff --git a/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/subfolder/subfolder.mixins.json b/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/subfolder/subfolder.mixins.json
new file mode 100644
index 0000000..ef124ca
--- /dev/null
+++ b/src/test/resources/projects/mixinApAutoRefmap/src/main/resources/subfolder/subfolder.mixins.json
@@ -0,0 +1,14 @@
+{
+  "required": true,
+  "minVersion": "0.8",
+  "package": "net.fabricmc.example.mixin",
+  "compatibilityLevel": "JAVA_16",
+  "mixins": [
+  ],
+  "client": [
+      "ExampleMixinSubfolder"
+  ],
+  "injectors": {
+    "defaultRequire": 1
+  }
+}