In this work we study genus one fibrations in Calabi-Yau three-folds with a non-trivial first fundamental group. The manifolds under consideration are constructed as smooth quotients of complete intersection Calabi-Yau three-folds (CICYs) by a freely acting, discrete automorphism. By probing the compatibility of symmetries with genus one fibrations (that is, discrete group actions which preserve a local decomposition of the manifold into fiber and base) we find fibrations that are inherited from fibrations on the covering spaces. Of the 7,890 CICY three-folds, 195 exhibit known discrete symmetries, leading to a total of 1,695 quotient manifolds. By scanning over 20,700 fiber/symmetry pairs on the covering spaces we find 17,161 fibrations on the quotient Calabi-Yau manifolds. It is found that the vast majority of the non-simply connected manifolds studied exhibit multiple different genus one fibrations -echoing a similar ubiquity of such structures that has been observed in other data sets. The results are available at [1]. The possible base manifolds are all singular and are catalogued. These Calabi-Yau fibrations generically exhibit multiple fibers and are of interest in F-theory as backgrounds leading to theories with superconformal loci and discretely charged matter.