The discontinuous Galerkin methods demonstrated to be well suited for scale resolving simulations of complex configurations, characterized by different fluid dynamics phenomena, such as transition, separation, shock/boundary layer interaction. Unfortunately, solvers based on these methods cannot yet reach the computational efficiency of well-established standard solvers, e.g., based on finite volume methods. To reduce the computational cost and the memory footprint, while not spoiling the accuracy, different approaches were investigated, which act on the spatial or the temporal discretization, and on the linear algebra. The above approaches have been extensively investigated, but rarely considering their mutual interactions. In this work, a p-adaptation algorithm is coupled with a time step-size adaptation algorithm to mitigate robustness issues arising after each adaptation cycle, probably related to the projection of the old solution on the new polynomial orders distribution. Moreover, this strategy is able to control the transient phase before each adaptation cycle, and can handle also the presence of initial steady solution, when the mesh is too coarse and the polynomial degree has not yet compensated for the lack of spatial accuracy. The effectiveness and accuracy of the proposed algorithm are demonstrated on transonic viscous flows with shock-wave/boundary-layer interaction.