This paper presents the results of the geoarchaeological study of a medieval motte known in historical documents as “Castrum Popilii” (Poviglio, Northern Italy). The Castrum Popilii motte, for its particular environmental characteristics, represents an exceptional case study for the Early Medieval Age in Po Valley. In 1989 an archaeological rescue excavation revealed an exceptionally well-preserved stratigraphic sequence at the northern side of the Santo Stefano church. The study of the archaeological materials and thin soil sections collected during this campaign, integrated with geoarchaeological observations, allowed the reconstruction of the natural and anthropogenic processes involved in the formation of the Santo Stefano di Poviglio stratigraphy sequence. The area also referred to as “Santo Stefano di Poviglio”, exposed the eastern limit of the medieval motte, characterizes by a sequence of occupation deposits, living floors, and wooden structural remains dated between the late 9th and the 11th centuries AD. The micromorphological study of this archaeological site led to developing a new hypothesis about the use of lime-based plaster in the construction of domestic living floors in a rural early medieval village in Central Po Plain. The sealing of the sequence due to the construction of a stone stronghold in the 15th century, combined with waterlogging, preserved the deposit from reworking by bioturbation and later human activities. On the other hand, water stagnation influenced a series of post-depositional migration and accumulation of iron–manganese and phosphatic features. The geoarchaeological tools applied in this study allowed to maximize the data collected in a rescue situation in 1989 highlighting new information about the genesis and development of Castrum Popilii medieval motte. •First micromorphological research conducted on an Early Medieval Motte in Northern Italy•Exceptional case of well-preserved Medieval stratigraphic sequence in Central Po Plain•Distinguish archaeological stratigraphic units through formation processes•Identification of living floors and occupational deposits related to a timber-framed house•The analyses performed highlighted new information about the use of impure lime-based plaster in an Early Medieval village