We present a general formalism that provides a systematic computation of the linear and non-linear perturbations for an arbitrary number of cosmological fluids in the early Universe going through various transitions, in particular the decay of some species (such as a curvaton or a modulus). Using this formalism, we revisit the question of isocurvature non-Gaussianities in the mixed inflaton-curvaton scenario and show that one can obtain significant non-Gaussianities dominated by the isocurvature mode while satisfying the present constraints on the isocurvature contribution in the observed power spectrum. We also study two-curvaton scenarios, taking into account the production of dark matter, and investigate in which cases significant non-Gaussianities can be produced.