Understanding the links between biodiversity and human aesthetic perception is vital for designing favourable urban environments and aligning conservation goals with well-being agendas. Despite evidence supporting the preference for beautiful and biodiverse landscapes, inconsistencies exist. This study aims to review the empirical literature on aesthetic perception and biodiversity research in urban settings and identify key methodological challenges in that area of study. The method used is a systematic mapping. The results revealed a lack of a unified methodology for operationalizing the concepts of biodiversity and aesthetic perception, as well as a shortage of standardized, evidence-based statistical procedures. These gaps hinder the systematic analysis of the relationship between biodiversity and perception and contribute to the incompatibility of biodiversity and perception levels. We propose strategies to address these challenges. This review aims to advance the integration of aesthetics and biodiversity science at the methodological level.