diff --git a/NEXT_CHANGELOG.md b/NEXT_CHANGELOG.md
index 969164d869..491321a48c 100644
--- a/NEXT_CHANGELOG.md
+++ b/NEXT_CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Notable Changes
 
 ### CLI
+* Skip non-exportable objects (e.g., `MLFLOW_EXPERIMENT`) during `workspace export-dir` instead of failing ([#4081](https://github.com/databricks/cli/issues/4081))
 
 ### Bundles
 
diff --git a/acceptance/cmd/workspace/export-dir-file-size-limit/output.txt b/acceptance/cmd/workspace/export-dir-file-size-limit/output.txt
index 6670e1be60..3d82b6fa68 100644
--- a/acceptance/cmd/workspace/export-dir-file-size-limit/output.txt
+++ b/acceptance/cmd/workspace/export-dir-file-size-limit/output.txt
@@ -1,9 +1,5 @@
 
 >>> [CLI] workspace export-dir /test-dir [TEST_TMP_DIR]/export
 Exporting files from /test-dir
-Warning: /test-dir/file.py (skipped; file too large)
-
-The following files were skipped because they exceed the maximum size limit:
-  - /test-dir/file.py (skipped; file too large)
-
+/test-dir/file.py (skipped; file too large)
 Export complete
diff --git a/acceptance/cmd/workspace/export-dir-skip-experiments/out.test.toml b/acceptance/cmd/workspace/export-dir-skip-experiments/out.test.toml
new file mode 100644
index 0000000000..d560f1de04
--- /dev/null
+++ b/acceptance/cmd/workspace/export-dir-skip-experiments/out.test.toml
@@ -0,0 +1,5 @@
+Local = true
+Cloud = false
+
+[EnvMatrix]
+  DATABRICKS_BUNDLE_ENGINE = ["terraform", "direct"]
diff --git a/acceptance/cmd/workspace/export-dir-skip-experiments/output.txt b/acceptance/cmd/workspace/export-dir-skip-experiments/output.txt
new file mode 100644
index 0000000000..78cf6e0a82
--- /dev/null
+++ b/acceptance/cmd/workspace/export-dir-skip-experiments/output.txt
@@ -0,0 +1,5 @@
+
+>>> [CLI] workspace export-dir /test-dir [TEST_TMP_DIR]/export
+Exporting files from /test-dir
+/test-dir/experiment (skipped; cannot export MLFLOW_EXPERIMENT)
+Export complete
diff --git a/acceptance/cmd/workspace/export-dir-skip-experiments/script b/acceptance/cmd/workspace/export-dir-skip-experiments/script
new file mode 100644
index 0000000000..b3876d60b8
--- /dev/null
+++ b/acceptance/cmd/workspace/export-dir-skip-experiments/script
@@ -0,0 +1,2 @@
+mkdir -p "$TEST_TMP_DIR/export"
+trace $CLI workspace export-dir /test-dir "$TEST_TMP_DIR/export"
diff --git a/acceptance/cmd/workspace/export-dir-skip-experiments/test.toml b/acceptance/cmd/workspace/export-dir-skip-experiments/test.toml
new file mode 100644
index 0000000000..da4c08d3ec
--- /dev/null
+++ b/acceptance/cmd/workspace/export-dir-skip-experiments/test.toml
@@ -0,0 +1,29 @@
+Local = true
+Cloud = false
+
+[Env]
+MSYS_NO_PATHCONV = "1"
+
+[[Server]]
+Pattern = "GET /api/2.0/workspace/list"
+Response.Body = '''
+{
+  "objects": [
+    {
+      "path": "/test-dir/experiment",
+      "object_type": "MLFLOW_EXPERIMENT",
+      "object_id": 125
+    }
+  ]
+}
+'''
+
+[[Server]]
+Pattern = "GET /api/2.0/workspace/get-status"
+Response.Body = '''
+{
+  "path": "/test-dir",
+  "object_type": "DIRECTORY",
+  "object_id": 123
+}
+'''
diff --git a/cmd/workspace/workspace/export_dir.go b/cmd/workspace/workspace/export_dir.go
index 8927be25c4..9bbbe10897 100644
--- a/cmd/workspace/workspace/export_dir.go
+++ b/cmd/workspace/workspace/export_dir.go
@@ -3,6 +3,7 @@ package workspace
 import (
 	"context"
 	"errors"
+	"fmt"
 	"io"
 	"io/fs"
 	"net/http"
@@ -24,7 +25,6 @@ type exportDirOptions struct {
 	sourceDir string
 	targetDir string
 	overwrite bool
-	warnings  []string
 }
 
 // isFileSizeError checks if the error is due to file size limits.
@@ -51,6 +51,26 @@ func isFileSizeError(err error) bool {
 	return false
 }
 
+// Object types that cannot be exported via the workspace export API.
+// These will be skipped with a warning during export-dir.
+var nonExportableTypes = []workspace.ObjectType{
+	workspace.ObjectTypeLibrary,
+	workspace.ObjectTypeDashboard,
+	workspace.ObjectTypeRepo,
+	// MLFLOW_EXPERIMENT is not defined as a constant in the SDK
+	workspace.ObjectType("MLFLOW_EXPERIMENT"),
+}
+
+// isNonExportable checks if an object type cannot be exported.
+func isNonExportable(objectType workspace.ObjectType) bool {
+	for _, t := range nonExportableTypes {
+		if objectType == t {
+			return true
+		}
+	}
+	return false
+}
+
 // The callback function exports the file specified at relPath. This function is
 // meant to be used in conjunction with fs.WalkDir
 func (opts *exportDirOptions) callback(ctx context.Context, workspaceFiler filer.Filer) func(string, fs.DirEntry, error) error {
@@ -77,6 +97,13 @@ func (opts *exportDirOptions) callback(ctx context.Context, workspaceFiler filer
 			return err
 		}
 		objectInfo := info.Sys().(workspace.ObjectInfo)
+
+		// Skip non-exportable objects (e.g., MLFLOW_EXPERIMENT, LIBRARY)
+		if isNonExportable(objectInfo.ObjectType) {
+			cmdio.LogString(ctx, fmt.Sprintf("%s (skipped; cannot export %s)", sourcePath, objectInfo.ObjectType))
+			return nil
+		}
+
 		targetPath += notebook.GetExtensionByLanguage(&objectInfo)
 
 		// Skip file if a file already exists in path.
@@ -92,9 +119,7 @@ func (opts *exportDirOptions) callback(ctx context.Context, workspaceFiler filer
 		if err != nil {
 			// Check if this is a file size limit error
 			if isFileSizeError(err) {
-				warning := sourcePath + " (skipped; file too large)"
-				cmdio.LogString(ctx, "Warning: "+warning)
-				opts.warnings = append(opts.warnings, warning)
+				cmdio.LogString(ctx, sourcePath+" (skipped; file too large)")
 				return nil
 			}
 			return err
@@ -140,7 +165,6 @@ func newExportDir() *cobra.Command {
 		w := cmdctx.WorkspaceClient(ctx)
 		opts.sourceDir = args[0]
 		opts.targetDir = args[1]
-		opts.warnings = []string{}
 
 		// Initialize a filer and a file system on the source directory
 		workspaceFiler, err := filer.NewWorkspaceFilesClient(w, opts.sourceDir)
@@ -159,16 +183,6 @@ func newExportDir() *cobra.Command {
 			return err
 		}
 
-		// Print all warnings at the end if any were collected
-		if len(opts.warnings) > 0 {
-			cmdio.LogString(ctx, "")
-			cmdio.LogString(ctx, "The following files were skipped because they exceed the maximum size limit:")
-			for _, warning := range opts.warnings {
-				cmdio.LogString(ctx, "  - "+warning)
-			}
-			cmdio.LogString(ctx, "")
-		}
-
 		return cmdio.RenderWithTemplate(ctx, newExportCompletedEvent(opts.targetDir), "", "Export complete\n")
 	}