In this work we solve the compressible Navier–Stokes equations written in primitive variables in order to simulate low Mach number aeroacoustic flows. We develop a Variational Multi-Scale formulation to stabilize the finite element discretization by including the orthogonal, dynamic and non-linear subscales, together with an implicit scheme for advancing in time. Three additional features define the proposed numerical scheme: the splitting of the pressure and temperature variables into a relative and a reference part, the definition of the matrix of stabilization parameters in terms of a modified velocity that accounts for the local compressibility, and the approximation of the dynamic stabilization matrix for the time dependent subscales. We also include a weak imposition of implicit non-reflecting boundary conditions in order to overcome the challenges that arise in the aeroacoustic simulations at low compressibility regimes. The order of accuracy of the method is verified for two- and three-dimensional linear and quadratic elements using steady manufactured solutions. Several benchmark flow problems are studied, including transient examples and aeroacoustic applications.