Plant-based pesticides are considered viable complements of conventional synthetic pesticides in agriculture. Their environmentally benign nature and potential to mitigate ecological impacts render them advantageous options for sustainable farming practices. However, the long-term effects of botanical pesticides on soil ecosystems remain unclear. This review aims to examine current evidence concerning the persistence of botanical pesticides in soil environments and their potential effects. Specifically, it addresses their biodegradation pathways in soil as well as their impact on soil enzymes and biology. The methodologies available to perform these studies are also briefly discussed, particularly focusing on how they can be tailored to improve the analysis of the impacts and challenges posed by the use of botanical pesticides in ecosystems.