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Understanding the effects of land-cover alterations on ecosystem functioning has become a major challenge in ecological research during the last decade. This has stimulated a rapid growth in research investigating the links between land-cover change and biotic interactions, but to date no study has evaluated the progress towards achieving this scientific goal. With the aim of identifying gaps in current knowledge and challenging research areas for the future, we reviewed the scientific literature published during the last decade (1998–2010) investigating land-cover change effects on trophically-mediated biotic interactions. Our results reveal a disproportionate focus on particular trophic interactions and ecosystem types. Furthermore, in most cases, the measurement of trophic interactions is carried out neglecting the identity of the interacting species and the interrelation between the type of land-cover change effects. Finally, inappropriate temporal scales are applied to cope with spatiotemporal resource fluctuations for the interacting species. We suggest that the ongoing patterns and trends of research hamper efforts to achieve a truly comprehensive understanding of the effects of land-cover alterations on trophic interactions, and hence on ecosystem functioning in human-impacted landscapes. We therefore recommend alternative research trends and indicate gaps in current knowledge that need to be filled. Furthermore, we highlight that these biases could also limit the effectiveness of management actions aimed at ensuring the resilience and long-term conservation of natural habitats worldwide.