We study exchange couplings in the organic magnets copper(II) phthalocyanine [Cu(II)Pc] and manganese(II) phthalocyanine [Mn(II)Pc] by a combination of Green's function perturbation theory and ab initio density-functional theory (DFT). Based on the indirect exchange model, our perturbation-theory calculation of Cu(II)Pc qualitatively agrees with the experimental observations. DFT calculations performed on Cu(II)Pc dimer show a very good quantitative agreement with exchange couplings that our theoretical group extracts by using a global fitting for the magnetization measurements to a spin-1/2 Bonner-Fisher model. These two methods give us remarkably consistent trends for the exchange couplings in Cu(II)Pc when changing the stacking angles. The situation is more complex for Mn(II)Pc owing to the competition between superexchange and indirect exchange.