Yes, according to Google, having all or part of your main content (MC) in iframes can negatively impact how Google indexes your content:

“Content displayed via iFrames may not be indexed and available to appear in Google’s search results. We recommend that you avoid the use of iFrames to display content. If you do include iFrames, make sure to provide additional text-based links to the content they display, so that Googlebot can crawl and index this content” source