Using the tight-binding approach coupled with mean-field Hubbard model, we theoretically study the effect of mechanical deformations on the magnetic properties of bilayer graphene (BLG) quantum dots (QDs). Results are obtained for AA- and AB(Bernal)-stacked BLG QDs, considering different geometries (hexagonal, triangular and square shapes) and edge types (armchair and zigzag edges). In the absence of strain, our results show that (i) the magnetization is affected by taking different dot sizes only for hexagonal BLG QDs with zigzag edges, exhibiting different critical Hubbard interactions, and (ii) the magnetization does not depend on the interlayer hopping energies, except for the geometries with zigzag edges and AA stacking. In the presence of in-plane and uniaxial strain, for all geometries we obtain two different magnetization regimes depending on the applied strain amplitude. The appearance of such different regimes is due to the breaking of layer and sublattice symmetries in BLG QDs.