The mechanism of proton conductivity in porous solids (i.e., Grotthuss or vehicular) is related to the structure and chemical environment of the pores. Direct observation of structure-function relationships is difficult because state-of-the-art solid proton conductors are often amorphous. Here, we present a systematic elucidation of two distinct proton transport pathways within MIT-25, a mesoporous metal-organic framework that exhibits parallel channels of similar to 27 angstrom and similar to 4.5 angstrom width. We characterize transport through these pores using temperature- and humidity-dependent proton conductivity measurements and density functional theory. Through control of vapor pressure we are able to sequentially fill the small and large pores, promoting proton conductivity with distinct activation energies at low and high relative humidity, respectively.