diff --git a/IPython/terminal/interactiveshell.py b/IPython/terminal/interactiveshell.py
index d14d5ea..22dc8c2 100644
--- a/IPython/terminal/interactiveshell.py
+++ b/IPython/terminal/interactiveshell.py
@@ -482,7 +482,10 @@ class TerminalInteractiveShell(InteractiveShell):
 
     @observe("shortcuts")
     def _shortcuts_changed(self, change):
-        user_shortcuts = change.new
+        if self.pt_app:
+            self.pt_app.key_bindings = self._merge_shortcuts(user_shortcuts=change.new)
+
+    def _merge_shortcuts(self, user_shortcuts):
         # rebuild the bindings list from scratch
         key_bindings = create_ipython_shortcuts(self)
 
@@ -568,7 +571,8 @@ class TerminalInteractiveShell(InteractiveShell):
         key_bindings = create_ipython_shortcuts(self, skip=shortcuts_to_skip)
         for binding in shortcuts_to_add:
             add_binding(key_bindings, binding)
-        self.pt_app.key_bindings = key_bindings
+
+        return key_bindings
 
     prompt_includes_vi_mode = Bool(True,
         help="Display the current vi mode (when using vi editing mode)."
@@ -607,8 +611,7 @@ class TerminalInteractiveShell(InteractiveShell):
             return
 
         # Set up keyboard shortcuts
-        key_bindings = create_ipython_shortcuts(self)
-
+        key_bindings = self._merge_shortcuts(user_shortcuts=self.shortcuts)
 
         # Pre-populate history from IPython's history database
         history = PtkHistoryAdapter(self)
diff --git a/IPython/terminal/tests/test_shortcuts.py b/IPython/terminal/tests/test_shortcuts.py
index a754ecf..ceab176 100644
--- a/IPython/terminal/tests/test_shortcuts.py
+++ b/IPython/terminal/tests/test_shortcuts.py
@@ -388,17 +388,19 @@ def test_modify_shortcut_with_filters(ipython_with_prompt):
     assert matched_keys == {")", "]", "}", "x", '"'}
 
 
-def test_command():
+def example_command():
     pass
 
 
 def test_add_shortcut_for_new_command(ipython_with_prompt):
-    matched = find_bindings_by_command(test_command)
+    matched = find_bindings_by_command(example_command)
     assert len(matched) == 0
 
-    with pytest.raises(ValueError, match="test_command is not a known"):
-        ipython_with_prompt.shortcuts = [{"command": "test_command", "new_keys": ["x"]}]
-    matched = find_bindings_by_command(test_command)
+    with pytest.raises(ValueError, match="example_command is not a known"):
+        ipython_with_prompt.shortcuts = [
+            {"command": "example_command", "new_keys": ["x"]}
+        ]
+    matched = find_bindings_by_command(example_command)
     assert len(matched) == 0
 
 
@@ -420,3 +422,13 @@ def test_add_shortcut_for_existing_command(ipython_with_prompt):
     ipython_with_prompt.shortcuts = []
     matched = find_bindings_by_command(skip_over)
     assert len(matched) == 5
+
+
+def test_setting_shortcuts_before_pt_app_init():
+    ipython = get_ipython()
+    assert ipython.pt_app is None
+    shortcuts = [
+        {"command": "IPython:auto_match.skip_over", "new_keys": ["x"], "create": True}
+    ]
+    ipython.shortcuts = shortcuts
+    assert ipython.shortcuts == shortcuts