Upcoming large-scale structure surveys can shed new light on the properties of dark energy. In particular, if dark energy is a dynamical component, it must have spatial perturbations. Their behaviour is regulated by the speed of sound parameter, which is currently unconstrained. In this work, we present the numerical methods that will allow to perform cosmological simulations of inhomogeneous dark energy scenarios where the speed of sound is small and non-vanishing. We treat the dark energy component as an effective fluid and build upon established numerical methods for hydrodynamics to construct a numerical solution of the effective continuity and Euler equations. In particular, we develop conservative finite volume schemes that rely on the solution of the Riemann problem, which we provide here in both exact and approximate forms for the case of a dark energy fluid.