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Decline in agricultural biodiversity (cultivated species and wild species used for food or that support agro-ecosystem functioning) at the farm scale has fueled concerns about potential negative effects of this biodiversity loss on the ecological and economic sustainability of agro-ecosystems. Despite these concerns, formal assessment of how agro-biodiversity has historically changed at scales larger than individual farms is fragmented. We quantified the changes in the abundance of 10 crop and livestock species, their overall diversity, and the way they were mixed in 'baskets' of agricultural products from 1911 to 2006, at a sub-regional (15 Regional County Municipalities) and regional scales. We found that the diversity of agricultural products increased at the regional scale. From 1911 to 1966, the region produced fodder, milk and maple, mixed in two low-diversity baskets. After 1966, the region provided a greater variety of baskets composed of newly introduced cash crops and high-value livestock. All baskets provided were themselves more diverse than historically and varied greatly in composition across space. Increasing regional diversity was related to changes in agricultural policy, while the variation in the composition of baskets produced was related to biophysical and socioeconomic characteristics. Our results indicate that agricultural transformations of the 21th century did not invariably lead to agro-biodiversity loss at large scales. We have also demonstrated that combining diversity measures at multiple scales with the analysis of compositional change of agricultural products over long time periods could improve research on the links between agro-biodiversity dynamics and resilience.