During the most recent webmaster hangout, Google employee John Mueller responded to a question about whether it is possible to sanction the use of pop-ups on mobile pages for a limited period of time, for example, a week.
According to Mueller, when these elements are “seen” by the algorithm responsible for toast notifications and interstitial ads, then Google can downgrade the corresponding pages in mobile search results. However, this is a rather weak ranking factor, notes SearchEngines.
After the pop-up notification is removed, Google will take this change into account the next time it crawls the URL and cancel the demotion.
That said, highly relevant content can rank well when using such elements. Therefore, this factor is really rather weak.
If your site needs to use a pop-up alert (which is not recommended), it is important to make sure that other content is also visible on the page, states NIX Solutions. Otherwise, Google will index the content of this window as main content.