Integrated micromorphology, plant macro, pollen, phytolith, and non-pollen palynomorph analyses from two 13 th century Teutonic Order castles, Karksi (Livonia), and Elbląg (Prussia), examine the livestock management and alimentation practices by the initial military colonisers during the Crusades. At Karksi, a key administrative centre in Livonia, in the area which later became the High Castle, the investigation of a midden and of the organic-rich sediment beneath allow the diachronic use of this area to be examined. Freshwater aquatic indicators are consistent with the occurrence of shallow stagnant water, as also suggested by a water-laid pond sediment identified in thin-section. Coprophilous spore taxa suggest the use of the pond as a watering hole. Plant macrofossils from the midden represent a range of habitats, mostly from wet/damp areas, as well as pastures and meadows, and also woodlands. Fragments of millet are embedded within herbivore dung in micromorphological thin-section showing the use of this grain as fodder. At Elbląg in Prussia, the initial Order headquarters, Trichuris sp. eggs may derive from animal feces as dung with parasite eggs was observed in thinsection, and a range of coprophilous taxa were extracted. The results from both sites show early colonisers use a mixed grain/leaf fodder diet for livestock, with a move to grain and grass later on. The results represent an important study of medieval castles from the period of active Crusading, and reveal the diachronicity of the range of livestock that the Teutonic Knights kept, whereabouts within the castles they were stabled, and livestock alimentation.