Ecofacts from a wooden structure and its surrounding area at the medieval Cathedral School site (Medieval period in Finland AD 1200-1520) were used to compliment the archaeological data from Turku, the oldest town of Finland. The site is of primary importance to the study of Turku’s past. The analysed ecofacts consisted primarily of vascular plant seeds, pollen, moss, invertebrates, and animal bones. Ecofact evidence proved that a wooden frame uncovered at the site was a latrine, dating to AD 1450–1520. Additionally, it was found out, that the older layer (AD 1350–1450) surrounding the latrine was part of a yard where domestic waste was being deposited. The results show that medieval residents at Turku had contacts overseas and the resources of local natural environment was exploited. The most interesting find is the presence of melegueta pepper (Aframomum melegueta L.), a plant native to West Africa, which had not been found in Finland before. In this study, the natural scientific analysis had an important role in the interpretations of archaeological features. These results deepen current knowledge of the medieval town of Turku, during an early phase of its urbanisation.