We prove the existence of many complete graphs in almost all sufficiently dense partitions obtained by an application of Szemerédi's Regularity Lemma. More precisely, we consider the number of complete graphs $K_{\ell}$ on $\ell$ vertices in $\ell$-partite graphs where each partition class consists of $n$ vertices and there is an $\varepsilon$-regular graph on $m$ edges between any two partition classes. We show that for all $\beta > $0, at most a $\beta^m$-fraction of graphs in this family contain less than the expected number of copies of $K_{\ell}$ provided $\varepsilon$ is sufficiently small and $m \geq Cn^{2-1/(\ell-1)}$ for a constant $C > 0$ and $n$ sufficiently large. This result is a counting version of a restricted version of a conjecture by Kohayakawa, Łuczak and Rödl and has several implications for random graphs.