In this work we consider the approximation of the isentropic Navier–Stokes equations. The model we present is capable of taking into account acoustic and flow scales at once. After space and time discretizations have been chosen, it is very convenient from the computational point of view to design fractional step schemes in time so as to permit a segregated calculation of the problem unknowns. While these segregation schemes are well established for incompressible flows, much less is known in the case of isentropic flows. We discuss this issue in this article and, furthermore, we study the way to weakly impose Dirichlet boundary conditions via Nitsche’s method. In order to avoid spurious reflections of the acoustic waves, Nitsche’s method is combined with a non-reflecting boundary condition. Employing a purely algebraic approach to discuss the problem, some of the boundary contributions are treated explicitly and we explain how these are included in the different steps of the final algorithm. Numerical evidence shows that this explicit treatment does not have a significant impact on the convergence rate of the resulting time integration scheme. The equations of the formulation are solved using a subgrid scale technique based on a term-by-term stabilization.