2

This defines my footline:

\setbeamercolor{footlinecolor}{fg=orange}
\renewcommand\footnoterule{{\color{orange}\hrule height 1pt width \paperwidth}}

\setbeamertemplate{footline}{%
  \footnoterule
    \includegraphics[height=10pt]{FAI.png}
    \hfill
    \scriptsize{\insertframenumber}
    \hfill
}

However, using the code above, the content of the slides can overlap the footline/footer/foot-logo.

Is there a way to prevent that (always force the content of a slide to lie above the logo and the footline/footer)?

1

If the content of your slide overlap your footnote, it is simply because you put too much content, it does not depend on the footline behavior.

One simple way to avoid such overlapping is to allow frame breaks with the option \begin{frame}[allowframebreaks]{The frame title}.

Another way, if you consider that your content can enter in the frame without break, is to add a small negative space to your slide (\vspace{-2em} for instance), do not hesitate to put them at the beginning or at the end, see https://tex.stackexchange.com/a/294402/97981 for another example where the overlap was at the top of the frame.

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