Motivated by the potential for application of organic semiconductors in flexible electronics, we present a theoretical study aiming at elucidating the interplay between mechanical strain and electronic, vibrational and charge transport properties of the prototypical high-mobility molecular semiconductor rubrene. Our study considers several factors that can play a role in the electro-mechanical response of a soft, van-der-Waals bonded, molecular crystal, such as intermolecular charge transfer integrals, lattice dynamics and electron phonon coupling. We find that compressive strain leads to an increase in magnitude of charge transfer integrals but also of the energetic disorder hampering the mobility. Charge transport simulations, based on the transient localization framework and fed with first-principles inputs, reveal a remarkably different response to strain applied along different crystal axes, in line with most recent experiments. The critical interplay between energetic disorder of intrinsic and extrinsic nature on the mobility-strain relationship is also discussed. The theoretical approach proposed in this work paves the way for the systematic study of the electro-mechanical response of different classes of high-mobility molecular semiconductors.