We define parabolic quasi-Coxeter elements in well generated complex reflection groups. We characterize them in multiple natural ways, and we study two combinatorial objects associated with them: the collections $\operatorname{Red}_W(g)$ of reduced reflection factorizations of $g$ and $\operatorname{RGS}(W,g)$ of the relative generating sets of $g$. We compute the cardinalities of these sets for large families of parabolic quasi-Coxeter elements and, in particular, we relate the size $\#\operatorname{Red}_W(g)$ with geometric invariants of Frobenius manifolds. This paper is second in a series of three; we will rely on many of its results in part III to prove uniform formulas that enumerate full reflection factorizations of parabolic quasi-Coxeter elements, generalizing the genus-$0$ Hurwitz numbers.