From the moment of arriving in the area of Torun, the Teutonic Knights began working on adapting the abandoned stronghold for defense purposes. The new seat was first surrounded by wood and earth fortifications and a stone wall, of which a fragment with a gate has remained to this day. The works advanced quickly and were so successful that in the years 1242-1246 the town was able to repel the attacks of the Prussians and prince Świętopełek. In these years, the so-called the first Prussian uprising, joined by the Pomeranian Duke. The insurgents then captured most of the Teutonic castles, except for Torun, Chelmno and Radzyn.
Around 1250, the Teutonic Knights considered it necessary to rise a brick castle. In the sources, we find information that in 1263 work was underway on the construction of the castle chapel, and all those who built it were to receive an indulgence from the bishop of Warmia – Anselm. In the same construction cycle, a refectory was built, and then a kitchen with a dormitory. Later, the eastern range was built with a dansker, chapter house, and cloisters, as well as the entire northwest range. We know the least about this wing of the castle, only a few mysterious rooms of unknown purpose have survived to our times, as well as the Zwinger and moat of the main castle, 10 to 13 m wide. The outer ward of the main castle was used to rise buildings with economic functions.