diff --git a/src/electron-main.ts b/src/electron-main.ts
index 488ec723..db6cd0af 100644
--- a/src/electron-main.ts
+++ b/src/electron-main.ts
@@ -364,6 +364,8 @@ app.enableSandbox();
 // We disable media controls here. We do this because calls use audio and video elements and they sometimes capture the media keys. See https://github.com/vector-im/element-web/issues/15704
 app.commandLine.appendSwitch("disable-features", "HardwareMediaKeyHandling,MediaSessionService");
 
+store.prepare(); // must be called before any async actions
+
 // Disable hardware acceleration if the setting has been set.
 if (store.get("disableHardwareAcceleration") === true) {
     console.log("Disabling hardware acceleration.");
diff --git a/src/i18n/strings/en_EN.json b/src/i18n/strings/en_EN.json
index 2bdb0bc9..22538512 100644
--- a/src/i18n/strings/en_EN.json
+++ b/src/i18n/strings/en_EN.json
@@ -19,6 +19,8 @@
         "zoom_out": "Zoom Out"
     },
     "common": {
+        "yes": "Yes",
+        "no":  "No",
         "about": "About",
         "brand_help": "%(brand)s Help",
         "help": "Help",
@@ -59,5 +61,12 @@
         "bring_all_to_front": "Bring All to Front",
         "label": "Window",
         "zoom": "Zoom"
+    },
+    "store": {
+        "error": {
+            "title": "Failed to load configuration",
+            "unsupported_backend_override": "TODO",
+            "unknown_backend_override": "TODO"
+        }
     }
 }
diff --git a/src/store.ts b/src/store.ts
index 5bfb6eab..c390a46f 100644
--- a/src/store.ts
+++ b/src/store.ts
@@ -16,7 +16,9 @@ limitations under the License.
 
 import ElectronStore from "electron-store";
 import keytar from "keytar-forked";
-import { app, safeStorage } from "electron";
+import { app, safeStorage, dialog, type SafeStorage } from "electron";
+
+import { _t } from "./language-helper.js";
 
 /**
  * Legacy keytar service names for storing secrets.
@@ -24,6 +26,20 @@ import { app, safeStorage } from "electron";
 const KEYTAR_SERVICE = "element.io";
 const LEGACY_KEYTAR_SERVICE = "riot.im";
 
+type SafeStorageBackend = ReturnType<SafeStorage["getSelectedStorageBackend"]>;
+
+/**
+ * Map of safeStorage backends to their command line arguments.
+ * kwallet6 cannot be specified via command line
+ * https://www.electronjs.org/docs/latest/api/safe-storage#safestoragegetselectedstoragebackend-linux
+ */
+const safeStorageBackendMap: Omit<Record<SafeStorageBackend, string>, "unknown" | "kwallet6"> = {
+    basic_text: "basic",
+    gnome_libsecret: "gnome-libsecret",
+    kwallet: "kwallet",
+    kwallet5: "kwallet5",
+};
+
 /**
  * JSON-backed store for settings which need to be accessible by the main process.
  * Secrets are stored within the `safeStorage` object, encrypted with safeStorage.
@@ -37,6 +53,10 @@ class Store extends ElectronStore<{
     locale?: string | string[];
     disableHardwareAcceleration: boolean;
     safeStorage?: Record<string, string>;
+    // Only known for Linux - the safeStorage backend used for the safeStorage data as written
+    safeStorageBackend?: SafeStorageBackend;
+    // Only valid for Linux - whether to override the safeStorage backend via commandLine
+    safeStorageBackendOverride?: boolean;
 }> {
     public constructor() {
         super({
@@ -69,37 +89,147 @@ class Store extends ElectronStore<{
                 safeStorage: {
                     type: "object",
                 },
+                safeStorageBackend: {
+                    type: "string",
+                },
+                safeStorageBackendOverride: {
+                    type: "boolean",
+                },
             },
         });
     }
 
-    private whenSafeStorageReadyPromise?: Promise<unknown>;
-    public async safeStorageReady(): Promise<void> {
-        if (!this.whenSafeStorageReadyPromise) {
-            this.whenSafeStorageReadyPromise = Promise.allSettled([app.whenReady().then(() => this.migrateSecrets())]);
+    /**
+     * Prepare the store, does not prepare safeStorage, which needs to be done after the app is ready.
+     * Must be executed in the first tick of the event loop so that it can call Electron APIs before ready state.
+     */
+    public prepare(): void {
+        if (process.platform === "linux") {
+            if (this.get("safeStorageBackendOverride")) {
+                const backend = this.get("safeStorageBackend")!;
+                if (backend in safeStorageBackendMap) {
+                    app.commandLine.appendSwitch(
+                        "password-store",
+                        safeStorageBackendMap[backend as keyof typeof safeStorageBackendMap],
+                    );
+                } else {
+                    // This case should never happen, but could due to a downgrade or a modified store.
+                    dialog.showErrorBox(_t("store|error|title"), _t("store|error|unsupported_backend_override"));
+                    throw new Error("safeStorage backend override is not supported");
+                }
+            }
         }
-        await this.whenSafeStorageReadyPromise;
+    }
+
+    private safeStorageReadyPromise?: Promise<unknown>;
+    public async safeStorageReady(): Promise<void> {
+        if (!this.safeStorageReadyPromise) {
+            this.safeStorageReadyPromise = this.prepareSafeStorage();
+        }
+        await this.safeStorageReadyPromise;
     }
 
     private getSecretStorageKey = (key: string) => `safeStorage.${key}` as const;
 
+    private async prepareSafeStorage(): Promise<void> {
+        await app.whenReady();
+
+        if (process.platform === "linux") {
+            // Linux safeStorage support is hellish, the support varies on the Desktop Environment used rather than the store itself.
+            // https://github.com/electron/electron/issues/39789 https://github.com/microsoft/vscode/issues/185212
+            let safeStorageBackend = this.get("safeStorageBackend");
+            const selectedSafeStorageBackend = safeStorage.getSelectedStorageBackend();
+
+            if (selectedSafeStorageBackend === "unknown") {
+                // This should never happen but good to be safe
+                dialog.showErrorBox(_t("store|error|title"), _t("store|error|unknown_backend_override"));
+                throw new Error("safeStorage backend unknown");
+            }
+
+            if (!safeStorageBackend) {
+                if (selectedSafeStorageBackend === "basic_text") {
+                    // Ask the user if they want to use plain text encryption
+                    // TODO should we only do this if they have existing data
+                    const { response } = await dialog.showMessageBox({
+                        // TODO
+                        title: "Error 1",
+                        message: "Message",
+                        // detail: _t(""),
+                        type: "question",
+                        buttons: [_t("common|no"), _t("common|yes")],
+                        defaultId: 0,
+                        cancelId: 0,
+                    });
+                    if (response === 0) {
+                        throw new Error("safeStorage backend basic_text and user rejected it");
+                    }
+                }
+
+                // Store the backend used for the safeStorage data so we can detect if it changes
+                this.set("safeStorageBackend", selectedSafeStorageBackend);
+                safeStorageBackend = selectedSafeStorageBackend;
+            } else if (safeStorageBackend !== selectedSafeStorageBackend) {
+                console.warn(`safeStorage backend changed from ${safeStorageBackend} to ${selectedSafeStorageBackend}`);
+
+                if (safeStorageBackend === "basic_text") {
+                    console.info(`Migrating safeStorage from basic_text to ${selectedSafeStorageBackend}`);
+                    const data = this.get("safeStorage");
+                    if (data) {
+                        for (const key in data) {
+                            const plaintext = data[key];
+                            await this.setSecret(key, plaintext);
+                        }
+                    }
+                } else if (safeStorageBackend in safeStorageBackendMap) {
+                    // Warn the user that the backend has changed and ask if they wish to use the old one
+                    const { response } = await dialog.showMessageBox({
+                        // TODO
+                        title: "Error 2",
+                        message: "Message",
+                        // detail: _t(""),
+                        type: "question",
+                        buttons: [_t("common|no"), _t("common|yes")],
+                        defaultId: 0,
+                        cancelId: 0,
+                    });
+                    if (response === 0) {
+                        throw new Error("safeStorage backend changed and user rejected mitigation");
+                    }
+                    this.set("safeStorageBackendOverride", true);
+                    app.relaunch();
+                } else {
+                    // Warn the user that the backend has changed and tell them that we cannot migrate
+                    // dialog.showErrorBox(_t(""), _t("")); TODO
+                    throw new Error("safeStorage backend changed and cannot migrate");
+                }
+            }
+
+            if (safeStorageBackend === "basic_text" && selectedSafeStorageBackend === safeStorageBackend) {
+                // TODO verify if this even works, the docstring makes it sound ephemeral!
+                safeStorage.setUsePlainTextEncryption(true);
+            }
+        }
+
+        if (!safeStorage.isEncryptionAvailable()) {
+            console.error("Store migration: safeStorage is not available");
+            throw new Error(`safeStorage is not available`);
+            // TODO fatal error
+        }
+
+        await this.migrateSecrets();
+    }
+
     /**
      * Migrates keytar data to safeStorage,
      * deletes data from legacy keytar but keeps it in the new keytar for downgrade compatibility.
-     * @throws if safeStorage is not available.
+     * @throws if safeStorage is not available. TODO
      */
     private async migrateSecrets(): Promise<void> {
-        if (this.has("safeStorage")) return;
+        if (this.has("safeStorage")) return; // already migrated
         console.info("Store migration: started");
-        if (
-            !safeStorage.isEncryptionAvailable() &&
-            !(process.platform === "linux" && safeStorage.getSelectedStorageBackend() === "basic_text")
-        ) {
-            console.error(
-                "Store migration: safeStorage is not available with backend",
-                safeStorage.getSelectedStorageBackend(),
-            );
-            throw new Error("safeStorage is not available");
+
+        if (process.platform === "linux" && safeStorage.getSelectedStorageBackend() === "basic_text") {
+            console.warn("Store migration: safeStorage is using basic text encryption");
         }
 
         try {