Despite global efforts to identify and classify species to improve biodiversity baselines, there still remains large knowledge shortfalls that affect our understanding of the functioning of ecosystems and the design of effective conservation practices. Using the results of the first ongoing large-scale biodiversity inventory for Chile which has already recorded ca. 1,800 species and discovered 87 new species of arthropods, we explore and discuss taxonomy (Linnean) and distribution (Wallacean) shortfalls that preclude large-scale knowledge of arthropod biodiversity for one of the lesser studied groups in the world — the arthropods. Linnean shortfalls are mainly associated with the lack of funding of monitoring and inventory initiatives and the bias towards most charismatic or umbrella species, which in turn trigger effects on the experts’ availability, recruitment of taxonomists in research centers, journal impact factors, as well as the availability of scientific collections of type specimens. Instead, Wallacean shortfalls are related to accessibility to remote areas, and the spatial and temporal resolution of sampling efforts. Based on our results and literature review, we discuss the findings and also propose a novel conceptual framework aimed to reduce data gaps and support biodiversity conservation policies, particularly in developing countries. The framework has three main components: (1) the ecosystems, their species, and the threats; (2) the key elements for a biodiversity assessment strategy, and (3) an action plan for protecting biodiversity.