Pepper (Capsicum spp.) is an important solanaceous cash crop in Benin; however, productivity is limited due to several key constraints, especially diseases caused by viruses. We sought to understand farmers’ perceptions of viral diseases, management strategies deployed, and to identify the virus population affecting pepper production in Benin. To assess farmers’ perceptions and management of viral diseases, a survey was carried out in four agroecological zones of Benin. A total of 144 pepper farmers were interviewed using the snowball method. A total of 52 pepper leaf samples with virus-like symptoms were collected and diagnosed by reverse-transcriptase polymerase chain reaction (RT-PCR) or PCR. Pepper production systems varied across agroecological zones (P ≤ 0.001) with a predominance of farms practicing monoculture (82%). The majority of farmers (89%) indicated that pests and diseases were the main constraints to increased production. Cucumber mosaic virus (92% of the total samples), Pepper vein yellow virus (52%), and Pepper veinal mottle virus (50%) were the major viruses detected in pepper fields in Benin. There were both single (29%) and mixed (71%) infections of the viruses, suggesting that mixed infections are common for pepper in Benin, confounding efforts to reduce virus infections. Nearly 100% of the farmers surveyed were not aware of these viral diseases. They also could not directly relate symptoms of virus infection to the presence of aphids, whiteflies, or thrips. Farmers relied primarily on synthetic insecticides (93%) to control virus vectors. Interestingly, some farmers applied commercial (12%) and homemade (17%) biopesticides, with neem-based preparations being the most widely used. A total of 15% of farmers used companion cropping with maize, mint or basil and 43% of farmers used crop rotation as a cultural management practice to control viral disease and vector pressure in pepper fields. The implications of this work include the importance of training farmers and extension agents on diagnosis of viruses and their vectors causing viral diseases. This study provides baseline information for the development of host-resistant cultivars and deployment of integrated pest management strategies for pepper in Benin to reduce farmer losses.