diff --git a/src/Lifecycle.js b/src/Lifecycle.js
index 0e2389fd1c..a7f90f847d 100644
--- a/src/Lifecycle.js
+++ b/src/Lifecycle.js
@@ -369,7 +369,7 @@ async function _doSetLoggedIn(credentials, clearStorage) {
     // If there's an inconsistency between account data in local storage and the
     // crypto store, we'll be generally confused when handling encrypted data.
     // Show a modal recommending a full reset of storage.
-    if (results.dataInLocalStorage && !results.dataInCryptoStore) {
+    if (results.dataInLocalStorage && results.cryptoInited && !results.dataInCryptoStore) {
         const signOut = await _showStorageEvictedDialog();
         if (signOut) {
             await _clearStorage();
diff --git a/src/MatrixClientPeg.js b/src/MatrixClientPeg.js
index cd40c7874e..7e93b1dd2e 100644
--- a/src/MatrixClientPeg.js
+++ b/src/MatrixClientPeg.js
@@ -121,6 +121,7 @@ class MatrixClientPeg {
             // check that we have a version of the js-sdk which includes initCrypto
             if (this.matrixClient.initCrypto) {
                 await this.matrixClient.initCrypto();
+                StorageManager.setCryptoInitialised(true);
             }
         } catch (e) {
             if (e && e.name === 'InvalidCryptoStoreError') {
diff --git a/src/utils/StorageManager.js b/src/utils/StorageManager.js
index 1c0931273b..d0fcd58106 100644
--- a/src/utils/StorageManager.js
+++ b/src/utils/StorageManager.js
@@ -50,11 +50,15 @@ export async function checkConsistency() {
 
     let dataInLocalStorage = false;
     let dataInCryptoStore = false;
+    let cryptoInited = false;
     let healthy = true;
 
     if (localStorage) {
         dataInLocalStorage = localStorage.length > 0;
         log(`Local storage contains data? ${dataInLocalStorage}`);
+
+        cryptoInited = localStorage.getItem("mx_crypto_initialised");
+        log(`Crypto initialised? ${cryptoInited}`);
     } else {
         healthy = false;
         error("Local storage cannot be used on this browser");
@@ -84,10 +88,11 @@ export async function checkConsistency() {
         track("Crypto store disabled");
     }
 
-    if (dataInLocalStorage && !dataInCryptoStore) {
+    if (dataInLocalStorage && cryptoInited && !dataInCryptoStore) {
         healthy = false;
         error(
-            "Data exists in local storage but not in crypto store. " +
+            "Data exists in local storage and crypto is marked as initialised " +
+            " but no data found in crypto store. " +
             "IndexedDB storage has likely been evicted by the browser!",
         );
         track("Crypto store evicted");
@@ -104,6 +109,7 @@ export async function checkConsistency() {
     return {
         dataInLocalStorage,
         dataInCryptoStore,
+        cryptoInited,
         healthy,
     };
 }
@@ -155,3 +161,15 @@ export function trackStores(client) {
         });
     }
 }
+
+/**
+ * Sets whether crypto has ever been successfully
+ * initialised on this client.
+ * StorageManager uses this to determine whether indexeddb
+ * has been wiped by the browser: this flag is saved to localStorage
+ * and if it is true and not crypto data is found, an error is
+ * presented to the user.
+ */
+export function setCryptoInitialised(cryptoInited) {
+    localStorage.setItem("mx_crypto_initialised", cryptoInited);
+}