Secondary contact between closely related species can have genetic consequences. Competition for essential resources may lead to divergence in heritable traits that reduces interspecific competition, thus leading to increased genetic divergence. Conversely, hybridization and backcrossing can lead to genetic convergence. Here we study a population of a hybrid species, the Italian sparrow (Passer italiae), before and after it came into secondary contact with one of its parent species, the Spanish sparrow (P. hispaniolensis), in 2013. We demonstrate clear consequences of interspecific competition: Italian sparrows became outcompeted from a popular feeding site by its parent species, resulting in poorer body condition and a significant drop in population size. Although no significant morphological change could be detected, after only 3 years of sympatry the Italian sparrows had diverged significantly from the Spanish sparrows across a set of 81 protein coding genes. These temporal genetic changes are mirrored by genetic divergence observed in older sympatric Italian sparrow populations within the same area of contact. Compared to microallopatric birds, sympatric ones are genetically more diverged from Spanish sparrows. Interestingly, all six significant outlier genes in the temporal or spatial comparison (i.e. those showing the greatest divergence from Spanish sparrows) have been found to be associated with learning and neural development in other species.