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ABSTRACT AimBeta diversity quantifies the similarity of ecological assemblages. Its increase, known as biotic homogenisation, can be a consequence of biological invasions. However, species occurrence (presence/absence) and abundance‐based analyses can produce contradictory assessments of the magnitude and direction of changes in beta diversity. Previous work indicates these contradictions should be less frequent in nature than in theory, but a growing number of empirical studies report discrepancies between occurrence‐ and abundance‐based approaches. Understanding if these discrepancies represent a few isolated cases or are systematic across a diversity of ecosystems would allow us to better understand the general patterns, mechanisms and impacts of biotic homogenisation. LocationUnited States. Time Period1963–2020. Major Taxa StudiedVascular plants. MethodsWe used a dataset of more than 70,000 vegetation survey plots to assess differences in biotic homogenisation with and without invasion using both occurrence‐ and abundance‐based metrics of beta diversity. We estimated taxonomic biotic homogenisation by comparing beta diversity of invaded and uninvaded plots with both classes of metrics and investigated the characteristics of the non‐native species pool that influenced the likelihood that these metrics disagree. ResultsIn 78% of plot comparisons, occurrence‐ and abundance‐based calculations agreed in direction, and the two metrics were generally well correlated. Our empirical results are consistent with previous theory. Discrepancies between the metrics were more likely when the same non‐native species was at high cover at both plots compared for beta diversity, and when these plots were spatially distant. Main ConclusionsIn about 20% of cases, our calculations revealed differences in direction (homogenisation vs. differentiation) when comparing occurrence‐ and abundance‐based metrics, indicating that the metrics are not interchangeable, especially when distances between plots are high and invader diversity is low. When data permit, combining the two approaches can offer insights into the role of invasions and extirpations in driving biotic homogenisation/differentiation.