The next generation mass probes will obtain information on non‐linear power spectra P(k, z) and their evolution, allowing us to investigate the nature of Dark Energy. To exploit such data we need high‐precision simulations, extending at least up to scales of k≃ 10 h Mpc−1, where the effects of baryons can no longer be neglected. In this paper, we present a series of large scale hydrodynamical simulations for ΛCDM and dynamical Dark Energy (dDE) models, in which the equation of state parameter is z dependent. The simulations include gas cooling, star formation and Supernovae feedback. They closely approximate the observed star formation rate and the observationally derived star/Dark Matter mass ratio in collapsed systems. Baryon dynamics cause spectral shifts exceeding 1 per cent at k > 2–3 h Mpc−1 compared to pure N‐body simulations in the ΛCDM simulations. This agrees with previous studies, although we find a smaller effect (∼50 per cent) on the power spectrum amplitude at higher k values. dDE exhibits similar behaviour, even though the dDE simulations produce ∼20 per cent less stars than the analogous ΛCDM cosmologies. Finally, we show that the technique introduced in Casarini et al. to obtain spectra for any w(z) cosmology from constant‐w models at any redshift still holds when gas physics is taken into account. While this relieves the need to explore the entire functional space of DE state equations, we illustrate a severe risk that future data analysis could lead to misinterpretation of the DE state equation.