Upon his return to Flanders, Coxie stayed in Mechelen and took on two pupils in his workshop. However, Mechelen had become a cultural wasteland while Antwerp offered attractive opportunities as many of the altarpieces which had been destroyed needed to be replaced and its leading history painters Frans Floris and Willem Key had just died. He completed an altarpiece in Antwerp in 1575 and was registered in the Guild of Saint Luke of Antwerp in 1578. He remained in Antwerp during the period from 1580 to 1585 when the city was governed by a Calvinist government. He was even able as a Catholic to obtain commissions from the local government, which was tolerant of Catholics. In 1585 he was registered as a tenant in the Kloosterstraat in Antwerp, while his house in Mechelen was rented out. After the Fall of Antwerp and the return of Spanish Catholic control over the city in 1585, Coxie immediately gained commissions from patrons in Mechelen, including the city government. The continued appreciation of the Spanish king for the elderly artist was demonstrated when in 1589, he granted him an annuity. Coxie continued painting even when he was over 90 years old.. His last work, dated 1592, was the , today in the Cathedral of St. Michael and St. Gudula in Brussels. This contains on the back of one of the side panels the only known portrait of Philip II painted by the artist. Shortly thereafter, he died after accidentally falling off a scaffold while working on the restoration of the "Judgment of Solomon" in the Antwerp City Hall that he had made nine years earlier for the Antwerp City Council.