The current impact on biodiversity and the sustainability of agri-food systems, driven by the mortality of honeybees, wild bees, and other pollinators due to the use of synthetic chemical pesticides and their lethal and sublethal effects, has guided research at laboratory, experimental field, real field, and modeling levels. These studies aim to clarify the cause–effect relationships resulting from exposure to lethal and sublethal doses of the main commercial pesticide formulations. Furthermore, these research findings provide a vantage point for key insights with both global and local applicability. Using a mixed methodological design combining scientometrics, qualitative content analysis, and expert consultation supported by specialized software tools, an in-depth analysis of scientific publications was conducted to identify research trends related to the effects of pesticide molecules on pollinators, including mortality, sublethal effects, and ecotoxicological impacts. The analysis included the identification of general and specific trends, as well as baselines and research fronts, through which critical factors were determined. These critical factors were mapped through a qualitative meta-analysis to delineate the main effects of Fipronil, and neonicotinoid use on 62 pollinator species reported in Colombia. Finally, a compendium of key global insights was generated to inform the design of local alternatives. In particular, we encourage the development of environmentally and pollinator-friendly pest management strategies (Integrated Pest and Pollinator Management, IPPM), as well as the establishment of baselines for research on the effects and interactions of existing and novel biological, chemical, and organic pesticides with pollinators and other biotic or abiotic stressors in specific agroecosystems. This research should also consider their influence on pollinator microbiota, gene expression, and long-term consequences for populations and ecosystems, with special attention to native pollinators.