diff --git a/modules/installer.nix b/modules/installer.nix
index 9294c2f..a29c95b 100644
--- a/modules/installer.nix
+++ b/modules/installer.nix
@@ -13,6 +13,7 @@ let
     else "\${XDG_STATE_HOME:-$HOME/.local/state}/home-manager/gcroots";
   stateFile = pkgs.writeText "flatpak-state.json" (builtins.toJSON {
     packages = map (builtins.getAttr "appId") cfg.packages;
+    overrides = cfg.overrides;
   });
   statePath = "${gcroots}/${stateFile.name}";
 
@@ -42,6 +43,40 @@ let
     fi
   '';
 
+  overridesDir =
+    if (installation == "system")
+    then "/var/lib/flatpak/overrides"
+    else "\${XDG_DATA_HOME:-$HOME/.local/share}/flatpak/overrides";
+  flatpakOverridesCmd = installation: {}: ''
+    # Update overrides that are managed by this module (both old and new)
+    mkdir -p ${overridesDir}
+    ${pkgs.jq}/bin/jq -r -n \
+      --argjson old "$OLD_STATE" \
+      --argjson new "$NEW_STATE" \
+      '$new.overrides + $old.overrides | keys[]' \
+      | while read -r APP_ID; do
+          OVERRIDES_PATH=${overridesDir}/$APP_ID
+          
+          # Transform the INI-like Flatpak overrides file into a workable JSON
+          if [[ -f $OVERRIDES_PATH ]]; then
+            ACTIVE=$(cat $OVERRIDES_PATH \
+              | ${pkgs.jc}/bin/jc --ini \
+              | ${pkgs.jq}/bin/jq 'map_values(map_values(split(";") | select(. != []) // ""))')
+          else
+            ACTIVE={}
+          fi
+
+          # Generate and save the updated overrides file
+          ${pkgs.jq}/bin/jq -r -n \
+            --arg app_id "$APP_ID" \
+            --argjson active "$ACTIVE" \
+            --argjson old_state "$OLD_STATE" \
+            --argjson new_state "$NEW_STATE" \
+            --from-file ${./overrides.jq} \
+            >$OVERRIDES_PATH
+        done
+  '';
+
   flatpakInstallCmd = installation: update: { appId, origin ? "flathub", commit ? null, ... }: ''
     ${pkgs.flatpak}/bin/flatpak --${installation} --noninteractive --no-auto-pin install \
         ${if update && commit == null then ''--or-update'' else ''''} ${origin} ${appId}
@@ -86,6 +121,9 @@ pkgs.writeShellScript "flatpak-managed-install" ''
   # Install packages
   ${mkFlatpakInstallCmd installation updateApplications cfg.packages}
 
+  # Configure overrides
+  ${flatpakOverridesCmd installation {}}
+
   # Save state
   ln -sf ${stateFile} ${statePath}
 ''
diff --git a/modules/options.nix b/modules/options.nix
index e061b99..62fff40 100644
--- a/modules/options.nix
+++ b/modules/options.nix
@@ -119,6 +119,23 @@ in
     '';
   };
 
+  overrides = mkOption {
+    type = with types; attrsOf (attrsOf (attrsOf (either str (listOf str))));
+    default = {};
+    description = lib.mdDoc ''
+      Applies the provided attribute set into a Flatpak overrides file with the
+      same structure, keeping externally applied changes
+    '';
+    example = literalExpression ''
+      {
+        # Array entries will be merged with externally applied values
+        "com.visualstudio.code".Context.sockets = ["wayland" "!x11" "!fallback-x11"];
+        # String entries will override externally applied values
+        global.Environment.LC_ALL = "C.UTF-8";
+      };
+    '';
+  };
+
   update = mkOption {
     type = with types; submodule updateOptions;
     default = { onActivation = false; auto = { enable = false; onCalendar = "weekly"; }; };
diff --git a/modules/overrides.jq b/modules/overrides.jq
new file mode 100644
index 0000000..0da9f02
--- /dev/null
+++ b/modules/overrides.jq
@@ -0,0 +1,42 @@
+# Convert entry value into array
+def values($value): if ($value | type) == "string" then [$value] else ($value // []) end;
+
+# State aliases
+  ($old_state.overrides[$app_id] // {}) as $old
+| ($new_state.overrides[$app_id] // {}) as $new
+
+# Map sections that exist in either active or new state (ignore old)
+| $active + $new | keys | map (
+  . as $section | {"section_key": $section, "section_value": (
+
+      # Map entries that exist in either active or new state (ignore old)
+      ($active[$section] // {}) + ($new[$section] // {}) | keys | map (
+        . as $entry | { "entry_key": $entry, "entry_value": (
+
+            # Entry value aliases
+              $active[$section][$entry] as $active_value
+            | $new[$section][$entry]    as $new_value
+            | $old[$section][$entry]    as $old_value
+
+            # Use new value if it is a string
+            | if ($new_value | type) == "string" then $new_value
+              else
+                # Otherwise remove old values from the active ones, and add the new ones
+                values($active_value) - values($old_value) + values($new_value)
+
+                # Remove empty arrays and duplicate values
+                | select(. != []) | unique
+                
+                # Convert array into Flatpak string array format
+                | join(";")
+              end
+          )}
+        )
+
+      # Remove empty arrays
+      | select(. != [])
+    )}
+  )[]
+
+# Generate the final overrides file
+| "[\(.section_key)]", (.section_value[] | "\(.entry_key)=\(.entry_value)"), ""