Cryptochrome 4a (Cry4a) is a leading candidate for the radical pair-based magnetoreceptor proposed toenable avian navigation. Following photoexcitation, electron transfer along a tryptophan tetrad generates radical pairs whose recombination dynamics are thought to underlie magnetic sensitivity. However, competing proton-related reactions that may modulate these spinselective processes remain poorly understood. Here, we combine classical molecular dynamics and quantum mechanical/molecular mechanical free energy simulations to investigate deprotonation of terminal tryptophan radical cations and a potential protoncoupled electron transfer (PCET) pathway involving a surface-exposed tyrosine. We find that limited solvent accessibility of the third tryptophan significantly suppresses its effective deprotonation, whereas the fourth tryptophan is more readily deprotonated despite similar intrinsic proton transfer thermodynamics. In addition, we identify a multisite PCET pathway in which electron transfer from tyrosine to the fourth tryptophan radical cation is coupled to proton transfer from tyrosine to interfacial water, with a free energy barrier consistent with sub-microsecond kinetics. These results demonstrate that proton transfer and PCET reactions at the protein-solvent interface can compete kinetically with radical pair recombination, thereby providing alternative pathways that may influence magnetic sensitivity. This work establishes a mechanistic framework for probing proton-coupled processes in cryptochrome-based magnetoreception.