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Abstract Urbanisation significantly influences ecological change, but its long-term effects on small mammal communities remain underexplored in Central Europe. This study examines temporal and spatial changes in small mammals across three urban zones (pericentral, peripheral, and suburban) in Nitra, Slovakia, across two trapping periods (2012–2015 and 2019–2024). A total of 1,519 individuals from 14 species were recorded, with higher abundance and species richness during the first period. The striped field mouse ( Apodemus agrarius ) was only detected in the second period, indicating a recent range expansion. Species diversity varied significantly among urban zones in both periods, with higher diversity in less urbanised areas. However, spatial differences in abundance were only significant during the first period, suggesting possible homogenisation over time. Community composition was greatly affected by both time and urban zone, with noticeable zone-specific changes. The results also indicate ongoing synanthropization, marked by a decline in forest-associated species and a rise in generalists and urban-tolerant taxa. Seasonal changes showed a similar pattern of capture success in all zones, with the highest success rate in autumn. These findings highlight the constantly changing nature of urban ecosystems, which may be of particular interest and stimulate further discussion about how urban structure, landscape context, and time influence small mammal communities. Long-term monitoring and ecologically informed urban planning are crucial for preserving biodiversity in these dynamic settings.