diff --git a/Riot/Modules/Application/LegacyAppDelegate.m b/Riot/Modules/Application/LegacyAppDelegate.m
index 3a617e915..b0119dfa0 100644
--- a/Riot/Modules/Application/LegacyAppDelegate.m
+++ b/Riot/Modules/Application/LegacyAppDelegate.m
@@ -1908,6 +1908,9 @@ NSString *const AppDelegateUniversalLinkDidChangeNotification = @"AppDelegateUni
             AppConfigService.shared.session = mxSession;
             [BWIAnalytics.sharedTracker setSessionWithSession:mxSession];
             
+            // bwi: #5158 update permalink prefix when session is running
+            [MXSDKOptions sharedInstance].clientPermalinkBaseUrl = AppConfigService.shared.permalinkUrl;
+            
             [MXSDKOptions sharedInstance].analyticsDelegate = BWIAnalytics.sharedTracker;
             [DecryptionFailureTracker sharedInstance].delegate = BWIAnalytics.sharedTracker;
         }
diff --git a/Riot/Modules/MatrixKit/Utils/MXKTools.m b/Riot/Modules/MatrixKit/Utils/MXKTools.m
index a93c09f93..73b7a97a5 100644
--- a/Riot/Modules/MatrixKit/Utils/MXKTools.m
+++ b/Riot/Modules/MatrixKit/Utils/MXKTools.m
@@ -69,7 +69,7 @@ static NSRegularExpression* permalinkRegex;
         htmlTagsRegex  = [NSRegularExpression regularExpressionWithPattern:@"<(\\w+)[^>]*>" options:NSRegularExpressionCaseInsensitive error:nil];
         linkDetector = [NSDataDetector dataDetectorWithTypes:NSTextCheckingTypeLink error:nil];
                 
-        NSString *permalinkPattern = [NSString stringWithFormat:@"%@%@", BWIBuildSettings.shared.clientPermalinkBaseUrl ?: kMXMatrixDotToUrl, kMXKToolsRegexStringForPermalink];
+        NSString *permalinkPattern = [NSString stringWithFormat:@"%@%@", AppConfigService.shared.permalinkUrl ?: kMXMatrixDotToUrl, kMXKToolsRegexStringForPermalink];
         permalinkRegex = [NSRegularExpression regularExpressionWithPattern:permalinkPattern options:NSRegularExpressionCaseInsensitive error:nil];
     });
 }
diff --git a/Riot/Modules/Pills/PillType.swift b/Riot/Modules/Pills/PillType.swift
index 68659bcd9..4ab204c88 100644
--- a/Riot/Modules/Pills/PillType.swift
+++ b/Riot/Modules/Pills/PillType.swift
@@ -26,7 +26,7 @@ enum PillType: Codable {
 @available (iOS 15.0, *)
 extension PillType {
     private static var regexPermalinkTarget: NSRegularExpression? = {
-        let clientBaseUrl = BWIBuildSettings.shared.clientPermalinkBaseUrl
+        let clientBaseUrl = AppConfigService.shared.permalinkUrl() ?? BWIBuildSettings.shared.clientPermalinkBaseUrl
         let pattern = #"\#(clientBaseUrl)(?:/.*)/#/(?:(?:room|user)/)?((?:@|!|#)[^@!#/?\s]*)/?((?:\$)[^\$/?\s]*)?"#
         return try? NSRegularExpression(pattern: pattern, options: .caseInsensitive)
     }()
diff --git a/bwi/AppConfig/AppConfigService.swift b/bwi/AppConfig/AppConfigService.swift
index 175aee42a..05acbfd10 100644
--- a/bwi/AppConfig/AppConfigService.swift
+++ b/bwi/AppConfig/AppConfigService.swift
@@ -188,6 +188,7 @@ extension UserDefaults
     }
     
     func permalinkUrl() -> String? {
+        ServerURLHelper.shared.selectedIndex = ServerURLHelper.shared.indexOf(self.serverUrl())
         if let url = appConfig.permalinkUrl {
             return "https://" + url
         }  else if let url = ServerURLHelper.shared.httpsPermalink() {
diff --git a/bwi/QRCode/PermalinkQRCodeScanner.swift b/bwi/QRCode/PermalinkQRCodeScanner.swift
index ef99bf4f9..c19b0a8bc 100644
--- a/bwi/QRCode/PermalinkQRCodeScanner.swift
+++ b/bwi/QRCode/PermalinkQRCodeScanner.swift
@@ -68,7 +68,8 @@ struct PermalinkQRCodeScanner: View {
     }
     
     private func checkQRCode() {
-        if !BWIBuildSettings.shared.clientPermalinkBaseUrl.isEmpty && qrCode.hasPrefix(BWIBuildSettings.shared.clientPermalinkBaseUrl) {
+        let permalinkURL = AppConfigService.shared.permalinkUrl() ?? BWIBuildSettings.shared.clientPermalinkBaseUrl
+        if !permalinkURL.isEmpty && qrCode.hasPrefix(permalinkURL) {
             presentationMode.wrappedValue.dismiss()
             DispatchQueue.main.asyncAfter(deadline: .now() + 1.0) {
                 if let url = NSURLComponents(string: qrCode)?.url {