You can use \iffootnote in combination with \AtEveryCitekey.
Here the example:
\RequirePackage{filecontents}
\begin{filecontents*}{\jobname.bib}
@book{test,
author="John Smith",
title="The title",
year=1099,
publisher="nobody",
}
\end{filecontents*}
\documentclass[12pt]{beamer}
\usepackage[backend=biber,style=authortitle]{biblatex}
\AtEveryCitekey{\iffootnote{\color{red}\scriptsize}{\color{blue}}}
\bibliography{\jobname}
\begin{document}
\begin{frame}
Text on the frame\footcite{test}\quad\cite{test}
\textbf{\bibname}
\printbibliography
\end{frame}
\end{document}
The command \citesetup is used in front of the cite-command. In such cases you can use:
\appto\citesetup{\Huge}
The test \iffootnote failse because citesetup is used before foot.. works. You can only test things like: \footnote{Bla \cite{..}}.

\renewcommand{\footnotesize}{\scriptsize}does the job. – pluton Aug 30 '11 at 13:50citesetup. This command stands before every cite-command. – Marco Daniel Aug 30 '11 at 13:58\footciteseparably inbiblatex" – Marco Daniel Sep 2 '11 at 4:30