Biopesticides obtained from renewable resources and associated with biodegradability have the potential to address resource limitations and environmental pollution, often caused by many conventional pesticides, due to the facility of natural products to run in natural nutrient cycles. Flavonoids are considered benign substitutes for pesticides, however, little comprehensive information of their pesticidal activities and critical evaluation of their associated advantages is available. Therefore, this systematic review assessed sources, structures, activities and the environmental fate of flavonoids on a basis of 201 selected publications. We identified 281 different flavonoids that were investigated for their pesticidal activity as either a pure compound or a flavonoid-containing extract, with quercetin, kaempferol, apigenin, luteolin and their glycosides as the most studied compounds. Agricultural or food waste, a potential sustainable source for flavonoids, represent 10.6% of the plant sources of flavonoids within these studies, showing the currently underutilization of these preferable feedstocks. Analysis of pesticidal activities and target organisms revealed a broad target spectrum for the class of flavonoids, including fungi, insects, plants, bacteria, algae, nematodes, molluscs and barnacles. Little information is available on the environmental fate and biodegradation of flavonoids, and a connection to studies investigating pesticidal activities is largely missing. Emerging from these findings is the need for comprehensive understanding of flavonoids pesticidal activities with emphasis on structural features that influence activity and target specificity to avoid risks for non-target organisms. Only if the target spectrum and environmental fate of a potential biopesticide are known it can serve as a benign substitute. Then, flavonoids can be integrated in a valorization process of agricultural and food waste shifting the extract-produce-consume linear chain to a more circular economy.