BiOIO3 photocatalysts exposing (010) and (100) surfaces show high efficiency in photocatalytic experiments thanks to an efficient charge separation: photogenerated electrons migrate to the (010) face, and holes move to the (100) one (F. Chen, et al.). However, if one considers the band alignment of the two thermodynamically most stable terminations of the (010) and (100) surfaces as derived from high‐level density functional theory calculations, the band alignment is opposite to the experiment even if the formation of an explicit (010)/(100) junction is considered. To reconcile theory with experiment, one has to invoke the formation of a junction between a less stable (010) surface termination with the most stable (100) one. New chemical bonds at the interface result in a thermodynamically stable system and a significant charge transfer. This junction not only provides the correct band alignment, but also a position of the energy levels that is fully consistent with the experiment. This shows that in order to rationalize the behavior of semiconducting materials where charge separation helps the photoactivity, one has to describe the formation of explicit interfaces with atomistic precision, and to take into account the overall thermodynamic stability of the system.