diff --git a/conference.js b/conference.js
index 918ea35be..7decf5221 100644
--- a/conference.js
+++ b/conference.js
@@ -923,6 +923,35 @@ export default {
             : isVideoMutedByUser(APP.store);
     },
 
+    /**
+     * Verify if there is an ongoing system audio sharing session and apply to the provided track
+     * as a AudioMixer effect.
+     *
+     * @param {*} localAudioTrack - track to which system audio track will be applied as an effect, most likely
+     * microphone local audio track.
+     */
+    async _maybeApplyAudioMixerEffect(localAudioTrack) {
+
+        // At the time of writing this comment there were two separate flows for toggling screen-sharing
+        // and system audio sharing, the first is the legacy method using the functionality from conference.js
+        // the second is used when both sendMultipleVideoStreams and sourceNameSignaling flags are set to true.
+        // The second flow uses functionality from base/conference/middleware.web.js.
+        // We check if system audio sharing was done using the first flow by verifying this._desktopAudioStream and
+        // for the second by checking 'features/screen-share' state.
+        const { desktopAudioTrack } = APP.store.getState()['features/screen-share'];
+        const currentDesktopAudioTrack = this._desktopAudioStream || desktopAudioTrack;
+
+        // If system audio is already being sent, mix it with the provided audio track.
+        if (currentDesktopAudioTrack) {
+            // In case system audio sharing was done in the absence of an initial mic audio track, there is no
+            // AudioMixerEffect so we have to remove system audio track from the room before setting it as an effect.
+            await room.replaceTrack(currentDesktopAudioTrack, null);
+            this._mixerEffect = new AudioMixerEffect(currentDesktopAudioTrack);
+            logger.debug('Mixing new audio track with existing screen audio track.');
+            await localAudioTrack.setEffect(this._mixerEffect);
+        }
+    },
+
     /**
      * Simulates toolbar button click for audio mute. Used by shortcuts and API.
      * @param {boolean} mute true for mute and false for unmute.
@@ -976,7 +1005,11 @@ export default {
                     // Rollback the audio muted status by using null track
                     return null;
                 })
-                .then(audioTrack => this.useAudioStream(audioTrack));
+                .then(async audioTrack => {
+                    await this._maybeApplyAudioMixerEffect(audioTrack);
+
+                    this.useAudioStream(audioTrack);
+                });
         } else {
             muteLocalAudio(mute);
         }
@@ -2572,13 +2605,7 @@ export default {
                     return stream;
                 })
                 .then(async stream => {
-                    // In case screen sharing audio is also shared we mix it with new input stream. The old _mixerEffect
-                    // will be cleaned up when the existing track is replaced.
-                    if (this._mixerEffect) {
-                        this._mixerEffect = new AudioMixerEffect(this._desktopAudioStream);
-
-                        await stream.setEffect(this._mixerEffect);
-                    }
+                    await this._maybeApplyAudioMixerEffect(stream);
 
                     return this.useAudioStream(stream);
                 })