Let D be the boundary operator defined by Atiyah, Patodi and Singer, acting on smooth even forms of a compact orientable Riemannian manifold M. In continuation of our previous study, we deal with the problem of computing explicitly the η invariant η = η(M) for any orientable compact flat manifold M. After giving an explicit expression for η(s) in the case of cyclic holonomy group, we obtain a combinatorial formula that reduces the computation to the cyclic case. We illustrate the method by determining η(0) for several infinite families, some of them having non-abelian holonomy groups. For cyclic groups of odd prime order p ≥ 7, η(s) can be expressed as a multiple of L χ (s), an L-function associated to a quadratic character mod p, while η(0) is a (non-zero) integral multiple of the class number h − p of the number field Q( √ − p). In the case of metacyclic groups of odd order pq, with p, q primes, we show that η(0) is a rational multiple of h − p .