diff --git a/jupyter_core/application.py b/jupyter_core/application.py
index e572888..8b55a8a 100644
--- a/jupyter_core/application.py
+++ b/jupyter_core/application.py
@@ -168,9 +168,17 @@ def ask():
 
     def migrate_config(self):
         """Migrate config/data from IPython 3"""
-        if os.path.exists(os.path.join(self.config_dir, "migrated")):
-            # already migrated
-            return
+        try:  # let's see if we can open the marker file
+            # for reading and updating (writing)
+            f_marker = open(os.path.join(self.config_dir, "migrated"), 'r+')  # noqa
+        except PermissionError:  # not readable and/or writable
+            return  # so let's give up migration in such an environment
+        except FileNotFoundError:  # cannot find the marker file
+            pass  # that means we have not migrated yet, so continue
+        else:  # if we got here without raising anything,
+            # that means the file exists
+            f_marker.close()
+            return  # so we must have already migrated -> bail out
 
         from .migrate import get_ipython_dir, migrate
 
diff --git a/jupyter_core/tests/test_migrate.py b/jupyter_core/tests/test_migrate.py
index 776b3cc..b86887e 100644
--- a/jupyter_core/tests/test_migrate.py
+++ b/jupyter_core/tests/test_migrate.py
@@ -11,6 +11,7 @@
 import pytest
 
 from jupyter_core import migrate as migrate_mod
+from jupyter_core.application import JupyterApp
 from jupyter_core.migrate import (
     migrate,
     migrate_config,
@@ -53,7 +54,7 @@ def env(request):
     def fin():
         """Cleanup test env"""
         env_patch.stop()
-        shutil.rmtree(td)
+        shutil.rmtree(td, ignore_errors=os.name == 'nt')
 
     request.addfinalizer(fin)
 
@@ -216,3 +217,31 @@ def test_migrate(env):
     migrate()
     assert os.path.exists(env["JUPYTER_CONFIG_DIR"])
     assert os.path.exists(env["JUPYTER_DATA_DIR"])
+
+
+def test_app_migrate(env):
+    shutil.copytree(dotipython, env["IPYTHONDIR"])
+    app = JupyterApp()
+    app.initialize([])
+    assert os.path.exists(env["JUPYTER_CONFIG_DIR"])
+    assert os.path.exists(env["JUPYTER_DATA_DIR"])
+
+
+def test_app_migrate_skip_if_marker(env):
+    shutil.copytree(dotipython, env["IPYTHONDIR"])
+    touch(pjoin(env["JUPYTER_CONFIG_DIR"], "migrated"), "done")
+    app = JupyterApp()
+    app.initialize([])
+    assert os.listdir(env["JUPYTER_CONFIG_DIR"]) == ["migrated"]
+    assert not os.path.exists(env["JUPYTER_DATA_DIR"])
+
+
+def test_app_migrate_skip_unwritable_marker(env):
+    shutil.copytree(dotipython, env["IPYTHONDIR"])
+    migrated_marker = pjoin(env["JUPYTER_CONFIG_DIR"], "migrated")
+    touch(migrated_marker, "done")
+    os.chmod(migrated_marker, 0)  # make it unworkable
+    app = JupyterApp()
+    app.initialize([])
+    assert os.listdir(env["JUPYTER_CONFIG_DIR"]) == ["migrated"]
+    assert not os.path.exists(env["JUPYTER_DATA_DIR"])