diff --git a/CHANGELOG.md b/CHANGELOG.md
index 466947cd..92b7524f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -68,8 +68,20 @@
   colors has not configured) is now done by linear RGB interpolation,
   rather than converting to HSL and adjusting the luminance
   ([#2006][2006]).
+* XKB: virtual modifiers are now ignored. This works around various
+  issues seen when running foot under mutter (GNOME) ([#2009][2009]):
+  - Some key combinations generating the wrong escape sequence in the
+    kitty keyboard protocol.
+  - some of foot's default shortcuts not working (mainly those using
+    `Mod1`) out of the box.
+  - **Note: if you have custom key bindings in `foot.ini` that
+    includes one or more of the `Alt`, `Meta`, `Super`, `Hyper`,
+    `NumLock`, `ScrollLock`, `LevelThree` or `LevelFive` modifiers,
+    you need to update them; i.e. remove the virtual modifier(s),
+    leaving only the real modifiers (`Mod1`, `Mod2` etc).**
 
 [2006]: https://codeberg.org/dnkl/foot/issues/2006
+[2009]: https://codeberg.org/dnkl/foot/issues/2009
 
 
 ### Deprecated
diff --git a/input.c b/input.c
index cbe8e1c7..abaac8eb 100644
--- a/input.c
+++ b/input.c
@@ -620,6 +620,54 @@ keyboard_keymap(void *data, struct wl_keyboard *wl_keyboard,
         if (seat->kbd.mod_num != XKB_MOD_INVALID)
             seat->kbd.kitty_significant |= 1 << seat->kbd.mod_num;
 
+
+        /*
+         * Create a mask of all "virtual" modifiers. Some compositors
+         * add these *in addition* to the "real" modifiers (Mod1,
+         * Mod2, etc).
+         *
+         * Since our modifier logic (both for internal shortcut
+         * processing, and e.g. the kitty keyboard protocol) makes
+         * very few assumptions on available modifiers, which keys map
+         * to which modifier etc, the presence of virtual modifiers
+         * causes various things to break.
+         *
+         * For example, if a foot shortcut is Mod1+b (i.e. Alt+b), it
+         * won't match if the compositor _also_ sets the Alt modifier
+         * (the corresponding shortcut in foot would be Alt+Mod1+b).
+         *
+         * See https://codeberg.org/dnkl/foot/issues/2009
+         *
+         * Mutter (GNOME) is known to set the virtual modifiers in
+         * addtiion to the real modifiers.
+         *
+         * As far as I know, there's no compositor that _only_ sets
+         * virtual modifiers (don't think that's even legal...?)
+         */
+        {
+            xkb_mod_index_t alt = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_ALT);
+            xkb_mod_index_t meta = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_META);
+            xkb_mod_index_t super = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_SUPER);
+            xkb_mod_index_t hyper = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_HYPER);
+            xkb_mod_index_t num_lock = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_NUM);
+            xkb_mod_index_t scroll_lock = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_SCROLL);
+            xkb_mod_index_t level_three = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_LEVEL3);
+            xkb_mod_index_t level_five = xkb_keymap_mod_get_index(seat->kbd.xkb_keymap, XKB_VMOD_NAME_LEVEL5);
+
+            xkb_mod_index_t ignore = 0;
+
+            if (alt != XKB_MOD_INVALID) ignore |= 1 << alt;
+            if (meta != XKB_MOD_INVALID) ignore |= 1 << meta;
+            if (super != XKB_MOD_INVALID) ignore |= 1 << super;
+            if (hyper != XKB_MOD_INVALID) ignore |= 1 << hyper;
+            if (num_lock != XKB_MOD_INVALID) ignore |= 1 << num_lock;
+            if (scroll_lock != XKB_MOD_INVALID) ignore |= 1 << scroll_lock;
+            if (level_three != XKB_MOD_INVALID) ignore |= 1 << level_three;
+            if (level_five != XKB_MOD_INVALID) ignore |= 1 << level_five;
+
+            seat->kbd.virtual_modifiers = ignore;
+        }
+
         seat->kbd.key_arrow_up = xkb_keymap_key_by_name(seat->kbd.xkb_keymap, "UP");
         seat->kbd.key_arrow_down = xkb_keymap_key_by_name(seat->kbd.xkb_keymap, "DOWN");
     }
@@ -1759,6 +1807,10 @@ keyboard_modifiers(void *data, struct wl_keyboard *wl_keyboard, uint32_t serial,
 {
     struct seat *seat = data;
 
+    mods_depressed &= ~seat->kbd.virtual_modifiers;
+    mods_latched &= ~seat->kbd.virtual_modifiers;
+    mods_locked &= ~seat->kbd.virtual_modifiers;
+
 #if defined(_DEBUG)
     char depressed[256];
     char latched[256];
diff --git a/wayland.h b/wayland.h
index 6215d708..37dd7860 100644
--- a/wayland.h
+++ b/wayland.h
@@ -136,6 +136,8 @@ struct seat {
         xkb_mod_mask_t legacy_significant;  /* Significant modifiers for the legacy keyboard protocol */
         xkb_mod_mask_t kitty_significant;   /* Significant modifiers for the kitty keyboard protocol */
 
+        xkb_mod_mask_t virtual_modifiers;   /* Set of modifiers to completely ignore */
+
         xkb_keycode_t key_arrow_up;
         xkb_keycode_t key_arrow_down;