Motivated by classical Alexander invariants of affine hypersurface complements, we endow certain finite dimensional quotients of the homology of abelian covers of complex algebraic varieties with a canonical and functorial mixed Hodge structure (MHS). More precisely, we focus on covers which arise algebraically in the following way: if U is a smooth connected complex algebraic variety and G is a complex semiabelian variety, the pullback of the exponential map by an algebraic morphism $f:U\to G$ yields a covering space $\pi :U^f\to U$ whose group of deck transformations is $\pi _1(G)$. The new MHSs are compatible with Deligne’s MHS on the homology of U through the covering map $\pi $ and satisfy a direct sum decomposition as MHSs into generalized eigenspaces by the action of deck transformations. This provides a vast generalization of the previous results regarding univariable Alexander modules by Geske, Maxim, Wang and the authors in [16, 17]. Lastly, we reduce the problem of whether the first Betti number of the Milnor fiber of a central hyperplane arrangement complement is combinatorial to a question about the Hodge filtration of certain MHSs defined in this paper, providing evidence that the new structures contain interesting information.