Predictions of complex flows remain a significant challenge for engineering systems. Computationally affordable predictions of turbulent flows generally require Reynolds-Averaged Navier–Stokes (RANS) simulations and Large-Eddy Simulation (LES), the predictive accuracy of which can be insufficient due to non-Boussinesq turbulence and/or unresolved multiphysics that preclude qualitative fidelity in certain regimes. For example, in turbulent combustion, flame–turbulence interactions can lead to inverse-cascade energy transfer, which violates the assumptions of many RANS and LES closures. We present an adjoint-based, solver-embedded data assimilation method to augment the RANS and LES equations using trusted data. This is accomplished using Python-native flow solvers that leverage differentiable programming techniques to construct the adjoint equations needed for optimization. We present applications to shock-tube ignition delay predictions, turbulent premixed jet flames, and shock-dominated nonequilibrium flows and discuss the potential of adjoint-based approaches for future machine learning applications.