We present a multiscale physical mechanism and a stochastic model of breathing transitions, which represent adsorption-induced structural transformations between large-pore and narrow-pore conformations in bistable metal–organic frameworks, such as MIL-53. We show that due to interplay between host framework elasticity and guest molecule adsorption, these transformations on the level of the crystal occur via layer-by-layer shear. We construct a simple Hamiltonian that describes the physics of host–host and host–guest interactions and show that a respective Monte Carlo simulation model qualitatively reproduces the experimentally observed features of breathing transitions.