Since its consolidation as a sub-discipline of ecology in the late 1990s, urban ecology has grown substantially, enhancing our understanding of how urbanization shapes biodiversity and how biodiversity adapts to urbanization. Inherently interdisciplinary in its scope and application, urban ecology is rooted in multiple theoretical and methodological foundations, potentially making the field overwhelming for newcomers as the key literature is scattered across multiple disciplines. Drawing on the collective expertise of editors and reviewers, we attempt to address common pitfalls noted in studies of biodiversity within urban ecosystems and suggest action items for both the new and experienced urban ecologist. Here, we present key concepts for framing hypothesis-based urban biodiversity research questions, conceptualizing urban settings, accounting for spatial and temporal scales, selecting study systems and meaningful explanatory variables for research questions, and recognizing the social-ecological nature of urban systems. We offer insights and examples, emphasizing the importance of rigorous urban ecological research without imposing constraints on innovation.