If the inflaton is a heavy scalar field, it may equilibrate slower thansome other degrees of freedom, e.g. non-Abelian gauge bosons. In this case,perturbations in the inflaton field and in a thermalplasma coexist from a given moment onwards. We derive a gauge-invariant setof three coupled equations governing the time evolution of such a system.Despite singular coefficients,a reliable numerical solution can be obtained for a longtime period, starting from phase oscillations inside the Hubble horizon,and extending until acoustic oscillations in a radiation-dominated universe.Benchmarks are illustrated from a “weak regime”,where perturbations have a quantum-mechanical origin but get dissipatedby interactions with the plasma. Among applications of our formalismcould be inhomogeneity-induced nucleations inpost-inflationary phase transitions, andthe production of scalar-induced gravitational waves.