Strain, both naturally occurring and deliberately engineered, can have a considerable effect on the structural and electronic properties of 2D and layered materials. Uniaxial or biaxial heterostrain modifies the stacking arrangement of bilayer graphene (BLG) which subsequently influences the electronic structure of the bilayer. Here, we use density functional theory (DFT) calculations to investigate the interplay between an external applied heterostrain and the resulting stacking in BLG. We determine how a strain applied to one layer is transferred to a second, 'free' layer and at what critical strain the ground-state AB-stacking is disrupted. To overcome limitations introduced by periodic boundary conditions, we consider an approximate system consisting of an infinite graphene sheet and an armchair graphene nanoribbon. We find that above a critical strain of ∼1%, it is energetically favourable for the free layer to be unstrained, indicating a transition between uniform AB-stacking and non-uniform mixed stacking. This is in agreement with a simple model estimate based on the individual energy contributions of strain and stacking effects. Our findings suggest that small levels of strain provide a platform to reversibly engineer stacking order and Moiré features in bilayers, providing a viable alternative to twistronics to engineer topological and exotic physical phenomena in such systems.