Nielsen proved that the maximum number of maximal independent sets (MIS's) of size $k$ in an $n$-vertex graph is asymptotic to $(n/k)^k$, with the extremal construction a disjoint union of $k$ cliques with sizes as close to $n/k$ as possible. In this paper we study how many MIS's of size $k$ an $n$-vertex graph $G$ can have if $G$ does not contain a clique $K_t$. We prove for all fixed $k$ and $t$ that there exist such graphs with $n^{\lfloor\frac{(t-2)k}{t-1}\rfloor-o(1)}$ MIS's of size $k$ by utilizing recent work of Gowers and B. Janzer on a generalization of the Ruzsa-Szemerédi problem. We prove that this bound is essentially best possible for triangle-free graphs when $k\le 4$.