This work presents gauge-equivariant architectures for flow-based sampling in fermionic lattice field theories using pseudofermions as stochastic estimators for the fermionic determinant. This is the default approach in state-of-the-art lattice field theory calculations, making this development critical to the practical application of flow models to theories such as QCD. Methods by which flow-based sampling approaches can be improved via standard techniques such as even/odd preconditioning and the Hasenbusch factorization are also outlined. Numerical demonstrations in two-dimensional U(1) and SU(3) gauge theories with $N_f=2$ flavors of fermions are provided.