diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index ba6f51fe..0954f3f8 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -11,7 +11,7 @@ lorenz-tiny = "4.0.2"
 mercury = "0.4.3.18"
 mercury-mixin = "0.2.2"
 loom-native = "0.2.0"
-unpick = "3.0.0-beta.9"
+unpick = "3.0.0-beta.13"
 
 # Plugins
 spotless = "7.2.1"
diff --git a/src/main/java/net/fabricmc/loom/task/AbstractRemapJarTask.java b/src/main/java/net/fabricmc/loom/task/AbstractRemapJarTask.java
index 585cb63c..8120e377 100644
--- a/src/main/java/net/fabricmc/loom/task/AbstractRemapJarTask.java
+++ b/src/main/java/net/fabricmc/loom/task/AbstractRemapJarTask.java
@@ -158,7 +158,7 @@ public abstract class AbstractRemapJarTask extends Jar {
 		final WorkQueue workQueue = getWorkerExecutor().noIsolation();
 
 		workQueue.submit(workAction, params -> {
-			params.getMainInputFile().set(getInputFile());
+			params.getInputFile().set(getInputFile());
 			params.getArchiveFile().set(getArchiveFile());
 
 			params.getSourceNamespace().set(getSourceNamespace());
@@ -199,7 +199,7 @@ public abstract class AbstractRemapJarTask extends Jar {
 	protected abstract Provider<? extends ClientEntriesService.Options> getClientOnlyEntriesOptionsProvider(SourceSet clientSourceSet);
 
 	public interface AbstractRemapParams extends WorkParameters {
-		RegularFileProperty getMainInputFile();
+		RegularFileProperty getInputFile();
 		RegularFileProperty getArchiveFile();
 
 		Property<String> getSourceNamespace();
@@ -263,24 +263,26 @@ public abstract class AbstractRemapJarTask extends Jar {
 			}
 		}
 
+		// Note: the inputFile parameter is the remapping input file.
+		// The main input jar is available in the parameters, but should not be used
+		// for remapping as it might be missing some files added manually to this task.
 		protected abstract void execute(Path inputFile) throws IOException;
 
 		protected void modifyJarManifest() throws IOException {
 			int count = ZipUtils.transform(outputFile, Map.of(Constants.Manifest.PATH, bytes -> {
 				var manifest = new Manifest(new ByteArrayInputStream(bytes));
-
-				if (!getParameters().getPlatform().get().isForgeLike()) {
-					getParameters().getJarManifestService().get().apply(manifest, getParameters().getManifestAttributes().get());
-					manifest.getMainAttributes().putValue(Constants.Manifest.MAPPING_NAMESPACE, getParameters().getTargetNamespace().get());
-				}
-
-				byte[] sourceManifestBytes = ZipUtils.unpackNullable(getParameters().getMainInputFile().get().getAsFile().toPath(), Constants.Manifest.PATH);
+				byte[] sourceManifestBytes = ZipUtils.unpackNullable(getParameters().getInputFile().get().getAsFile().toPath(), Constants.Manifest.PATH);
 
 				if (sourceManifestBytes != null) {
 					var sourceManifest = new Manifest(new ByteArrayInputStream(sourceManifestBytes));
 					mergeManifests(manifest, sourceManifest);
 				}
 
+				if (!getParameters().getPlatform().get().isForgeLike()) {
+					getParameters().getJarManifestService().get().apply(manifest, getParameters().getManifestAttributes().get());
+					manifest.getMainAttributes().putValue(Constants.Manifest.MAPPING_NAMESPACE, getParameters().getTargetNamespace().get());
+				}
+
 				ByteArrayOutputStream out = new ByteArrayOutputStream();
 				manifest.write(out);
 				return out.toByteArray();
diff --git a/src/test/groovy/net/fabricmc/loom/test/integration/RemapJarContentsTest.groovy b/src/test/groovy/net/fabricmc/loom/test/integration/RemapJarContentsTest.groovy
index fdf556b5..85bb2e46 100644
--- a/src/test/groovy/net/fabricmc/loom/test/integration/RemapJarContentsTest.groovy
+++ b/src/test/groovy/net/fabricmc/loom/test/integration/RemapJarContentsTest.groovy
@@ -51,6 +51,10 @@ class RemapJarContentsTest extends Specification implements GradleProjectTestTra
 		ZipUtils.contains(gradle.getOutputFile('fabric-example-mod-1.0.0-sources.jar').toPath(), 'test_src_file.txt')
 		def manifest = readManifest(gradle.getOutputFile('fabric-example-mod-1.0.0.jar'))
 		manifest.mainAttributes.getValue('Hello-World') == 'test'
+		manifest.mainAttributes.getValue('Inherited-In-Remap-Jar') == '1234'
+		manifest.getAttributes('fabric.mod.json').getValue('Inherited-In-Remap-Jar') == '5678'
+		manifest.getAttributes('modid.mixins.json').getValue('Hello-World') == 'another test'
+		manifest.getAttributes('modid.mixins.json').getValue('Inherited-In-Remap-Jar') == '9'
 
 		where:
 		version << STANDARD_TEST_VERSIONS
diff --git a/src/test/resources/projects/remapJarContents/build.gradle b/src/test/resources/projects/remapJarContents/build.gradle
index b8b56edf..d7a60cc0 100644
--- a/src/test/resources/projects/remapJarContents/build.gradle
+++ b/src/test/resources/projects/remapJarContents/build.gradle
@@ -78,11 +78,21 @@ publishing {
 	}
 }
 
+jar {
+	manifest {
+		attributes 'Inherited-In-Remap-Jar': '1234'
+		attributes(['Inherited-In-Remap-Jar': '5678'], 'fabric.mod.json') // category not present in remapJar
+		attributes(['Inherited-In-Remap-Jar': '9'], 'modid.mixins.json') // category present in remapJar
+		attributes 'Hello-World': 'shadowed in remapJar'
+	}
+}
+
 remapJar {
 	from 'test_file.txt'
 
 	manifest {
 		attributes 'Hello-World': 'test'
+		attributes(['Hello-World': 'another test'], 'modid.mixins.json')
 	}
 }