When lattice QCD is formulated in sectors of fixed quark numbers, the canonical fermion determinants can be expressed explicitly in terms of transfer matrices. This in turn provides a complete factorization of the fermion determinants in temporal direction. Here we present a generic overview of this factorization, apply it to Wilson-type fermions and provide explicit constructions of the transfer matrices. Possible applications of the factorization include multi-level integration schemes and the construction of improved estimators for generic $n$-point correlation functions.