The pseudofermion functional renormalization group (pf-FRG) has been put forward as a semi-analytical scheme that, for a given microscopic spin model, allows to discriminate whether the low-temperature states exhibit magnetic ordering or a tendency towards the formation of quantum spin liquids. However, the precise nature of the putative spin liquid ground state has remained hard to infer from the original (single-site) pf-FRG scheme. Here we introduce a cluster pf-FRG approach, which allows for a more stringent connection between a microscopic spin model and its low-temperature spin liquid ground states. In particular, it allows to calculate spatially structured fermion bilinear expectation values on spatial clusters, which are formed by splitting the original lattice into several sublattices, thereby allowing for the positive identification of a family of bilinear spin liquid states. As an application of this cluster pf-FRG approach, we consider the $J_1$-$J_2$ SU($N$)-Heisenberg model on a square lattice, which is a paradigmatic example for a frustrated quantum magnet exhibiting quantum spin liquid behavior for intermediate coupling strengths. In the well-established large-$N$ limit of this model, we show that our approach correctly captures the emergence of the $pi$-flux spin liquid state at low temperatures. For small $N$, where the precise nature of the ground state remains controversial, we focus on the widely studied case of $N=2$, for which we determine the low-temperature phase diagram near the strongly-frustrated regime after implementing the fermion number constraint by the flowing Popov-Fedotov method. Our results suggest that the $J_1$-$J_2$-Heisenberg model does not support the formation of a fermion bilinear spin liquid state.