Over recent decades, quantum effects such as coherent electronic energy transfers, electron and hydrogen tunneling have been uncovered in biological processes. In this Perspective, we highlight some of the main conceptual and methodological tools employed in the field to investigate electron tunneling in proteins, with a particular emphasis on the methodologies we are currently developing. In particular, we describe our recent contributions to the development of a mixed quantum-classical framework aimed at describing physical systems lying at the border between the quantum and semi-classical worlds. We present original results obtained by combining our approach with constrained Density Functional Theory calculations. Moving to coarser levels of description, we summarize our latest findings on electron transfer between two redox proteins, thereby showing the stabilization of inter-protein, water-mediated, electron-transfer pathways.