diff --git a/CHANGELOG.md b/CHANGELOG.md
index 965d28fec8..46736592ee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,7 +2,9 @@
 
 ## [Unreleased]
 
-- No changes yet.
+- Fix archive and git inputs so that `--path` and `--exclude-path` paths are relative to
+  the `#subdir` rather than the root of the input. This fixes an unintended behavior change
+  that was introduced in `v1.32.0`.
 
 ## [v1.32.0] - 2024-05-16
 
diff --git a/data/template/buf.go.gen.yaml b/data/template/buf.go.gen.yaml
index b63d77f4d0..ec1d8f1721 100644
--- a/data/template/buf.go.gen.yaml
+++ b/data/template/buf.go.gen.yaml
@@ -23,9 +23,9 @@ inputs:
     tag: v27.0-rc1
     subdir: src
     paths:
-     - src/google/protobuf/cpp_features.proto
+     - google/protobuf/cpp_features.proto
   - git_repo: https://github.com/protocolbuffers/protobuf.git
     tag: v27.0-rc1
     subdir: java/core/src/main/resources
     paths:
-     - java/core/src/main/resources/google/protobuf/java_features.proto
+     - google/protobuf/java_features.proto
diff --git a/private/buf/buffetch/internal/reader.go b/private/buf/buffetch/internal/reader.go
index d403e94e9e..3457658d06 100644
--- a/private/buf/buffetch/internal/reader.go
+++ b/private/buf/buffetch/internal/reader.go
@@ -573,6 +573,15 @@ func getReadBucketCloserForBucket(
 	if err := validatePaths(inputSubDirPath, targetPaths, targetExcludePaths); err != nil {
 		return nil, nil, err
 	}
+	// For archive and git refs, target paths and target exclude paths are expected to be
+	// mapped to the inputSubDirPath rather than the execution context.
+	// This affects buftarget when checking and mapping paths against the controlling
+	// workspace, so we need to ensure that all paths are properly mapped.
+	targetPaths, targetExcludePaths = mapTargetPathsAndTargetExcludePathsForArchiveAndGitRefs(
+		inputSubDirPath,
+		targetPaths,
+		targetExcludePaths,
+	)
 	bucketTargeting, err := buftarget.NewBucketTargeting(
 		ctx,
 		logger,
@@ -904,6 +913,29 @@ func validatePaths(
 	return nil
 }
 
+func mapTargetPathsAndTargetExcludePathsForArchiveAndGitRefs(
+	inputSubDirPath string,
+	targetPaths []string,
+	targetExcludePaths []string,
+) ([]string, []string) {
+	// No need to remap
+	if inputSubDirPath == "." {
+		return targetPaths, targetExcludePaths
+	}
+	return slicesext.Map(
+			targetPaths,
+			func(targetPath string) string {
+				return normalpath.Join(inputSubDirPath, targetPath)
+			},
+		),
+		slicesext.Map(
+			targetExcludePaths,
+			func(targetExcludePath string) string {
+				return normalpath.Join(inputSubDirPath, targetExcludePath)
+			},
+		)
+}
+
 type getFileOptions struct {
 	keepFileCompression bool
 }
diff --git a/private/buf/cmd/buf/workspace_test.go b/private/buf/cmd/buf/workspace_test.go
index 2d5c4f9b73..87a88f0af0 100644
--- a/private/buf/cmd/buf/workspace_test.go
+++ b/private/buf/cmd/buf/workspace_test.go
@@ -291,7 +291,7 @@ func TestWorkspaceArchiveDir(t *testing.T) {
 			"lint",
 			filepath.Join(zipDir, "archive.zip#subdir=proto"),
 			"--path",
-			filepath.Join("proto", "rpc.proto"),
+			filepath.Join("rpc.proto"),
 		)
 	}
 }
@@ -342,7 +342,7 @@ func TestWorkspaceNestedArchive(t *testing.T) {
 			"lint",
 			filepath.Join(zipDir, "archive.zip#subdir=proto/internal"),
 			"--path",
-			filepath.Join("proto", "internal", "internal.proto"),
+			filepath.Join("internal.proto"),
 		)
 	}
 }
diff --git a/private/buf/cmd/buf/workspace_unix_test.go b/private/buf/cmd/buf/workspace_unix_test.go
index 8cdfa31200..aedf998624 100644
--- a/private/buf/cmd/buf/workspace_unix_test.go
+++ b/private/buf/cmd/buf/workspace_unix_test.go
@@ -160,7 +160,7 @@ func TestWorkspaceGit(t *testing.T) {
 		"build",
 		"../../../../.git#ref=HEAD,subdir=private/buf/cmd/buf/testdata/workspace/success/dir/proto",
 		"--path",
-		filepath.Join("private", "buf", "cmd", "buf", "testdata", "workspace", "success", "dir", "proto", "rpc.proto"),
+		filepath.Join("rpc.proto"),
 	)
 	testRunStdout(
 		t,
@@ -188,7 +188,7 @@ func TestWorkspaceGit(t *testing.T) {
 		"lint",
 		"../../../../.git#ref=HEAD,subdir=private/buf/cmd/buf/testdata/workspace/success/dir/proto",
 		"--path",
-		filepath.Join("private", "buf", "cmd", "buf", "testdata", "workspace", "success", "dir", "proto", "rpc.proto"),
+		filepath.Join("rpc.proto"),
 	)
 	testRunStdout(
 		t,
@@ -206,7 +206,7 @@ func TestWorkspaceGit(t *testing.T) {
 		"build",
 		"../../../../.git#ref=HEAD,subdir=private/buf/cmd/buf/testdata/workspace/success/v2/dir/proto",
 		"--path",
-		filepath.Join("private", "buf", "cmd", "buf", "testdata", "workspace", "success", "v2", "dir", "proto", "rpc.proto"),
+		filepath.Join("rpc.proto"),
 	)
 	testRunStdout(
 		t,
@@ -234,6 +234,6 @@ func TestWorkspaceGit(t *testing.T) {
 		"lint",
 		"../../../../.git#ref=HEAD,subdir=private/buf/cmd/buf/testdata/workspace/success/v2/dir/proto",
 		"--path",
-		filepath.Join("private", "buf", "cmd", "buf", "testdata", "workspace", "success", "v2", "dir", "proto", "rpc.proto"),
+		filepath.Join("rpc.proto"),
 	)
 }