By Using interstitial (popups) on the webiste, will google penalize ranks for desktop and mobile both ?
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We have implemented interstitials (pop-ups) on a website (Business Articles Website). The popups are basically used for getting leads from the website (using Signup popups).
Before Popup implementation the traffic was steady, After the implementation, the traffic started to decay after a couple of weeks and due to the drop we disabled the popup from the website and initiated a force crawl and within next few weeks, we observed traffic gaining back to its normal trend.
Within these timelines drop in desktop traffic was more and mobile traffic remain steady. As per Google guidelines, interstitials are more likely to be affected on mobile than desktop. But in our case, desktop traffic was hit more than mobile. So we carried out this experiment for 3 months. And we observed traffic decay and regain.
Is interstitials the only culprit here (as the drop is only in desktop) or Can there be some other reasons as well for the traffic drop?
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It seems likely that the interstitial is at least contributing to this pattern given the correlation during your test and given the fact that Google has specifically noted that they view interstitial pop-ups (at least certain implementations) as detrimental to the user experience. It is also possible that it isn't the interstitial itself that is raising a red flag as a ranking signal, but some other related issue (for instance, if the interstitial causes a significant page load delay, higher bounce rate, or if there is some rendering issue caused by the implementation of the pop-up).
As you note, if the interstitial is the issue, I would have expected it to affect mobile primarily and desktop less so - so the fact that the result is the opposite is surprising and may indicate a different cause for the traffic dips. I assume that you have compared this data not just WoW but YoY and are certain that the pattern isn't seasonal.
We do know, however, that Google is starting to move in the direction of mobile first in how they rank sites, making the mobile index and experience their primary source for rankings of both mobile and desktop versions.
In any case I would recommend testing a version of your pop-up which is not of a type that Google would consider "intrusive" (see this post for more detail: http://searchengineland.com/google-confirms-rolling-mobile-intrusive-interstitials-penalty-yesterday-267408) or adding a trigger to it (so for instance, don't show the popup immediately but only if the user scrolls a certain percentage of the page, or remains on the page for a set period of time).
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