We show that topology of the low-energy band structure in bilayer graphene critically depends on mechanical deformations of the crystal which may easily develop in suspended graphene flakes. We describe the Lifshitz transition that takes place in strained bilayers upon splitting the parabolic bands at intermediate energies into several Dirac cones at the energy scale of a few meV. Then, we show how this affects the electron Landau level spectra and the quantum Hall effect.