Pesticide use has grown rapidly in West Africa over the past decades. Regulatory capacity has not kept pace with the rapid proliferation of pesticide products and on-farm use. As a result, health and environmental impacts from the growing use of pesticides, despite their potential importance to food safety, remain largely unmonitored, underreported, and poorly understood by key stakeholders. This study protocol was the document for conducting a pesticide survey study to identify the most critically emerging pesticides across the Continent of Africa. Multiple countries were selected in this study to represent the north, east, south, and west regions of Africa. Two food commodities, maize and tomato, were chosen to monitor the pesticide level for food safety. This study protocol describes the fieldwork and laboratory work per the standards of Good Laboratory Practices (GLP) and ISO-17025 and US EPA 860 Residue Chemistry Guidelines but the survey study performed was not considered as a GLP or ISO 17025 study. This is because many steps were not able to be closely monitored per the GLP requirements. This protocol describes the requirements for a pesticide residue study in food collected from local markets. This protocol describes the test commodities, sampling methods, sample transfer/shipping, storage stability, sample analysis, sample disposal, and documentation and record keeping.