Modern wind turbines experience uneven inflow conditions across the rotor, due to the ambient flow’s shear and thermal stratification. Such conditions alter the shape and length of turbine wakes and thus impact the loads and power generation of downstream turbines. To this end, understanding the spatial evolution of the individual wakes under different atmospheric conditions is key to controlling and optimising turbine arrays. With this numerical study we aim to obtain a better understanding of the fundamental physics governing the near-wake dynamics of wind turbines under shear and thermal stability, by examining their tip-vortex breakup mechanisms. Our approach considers scale-resolving simulations of a single turbine wake under a linear shear profile as well as the application of harmonic tip perturbations to trigger flow instabilities. For the subsequent analysis we use the proper orthogonal decomposition (POD) method to extract coherent structures from the flow, and we also calculate mean kinetic energy fluxes to quantify each coherent structure’s contribution to wake recovery. The wake’s helical spiral is found to hinder wake recovery for all studied ambient flow conditions, whereas the mutual inductance instability has positive MKE flux leading to an enhanced wake recovery. Finally, the ambient shear has the largest impact on the local MKE flux with respect to downstream location by changing the shape of the curve and location of extrema, whereas thermal stratification has only a minimal impact on the magnitude of the near-wake local MKE flux distribution.