Background The connection between malaria-associated morbidities and farming activities has not been succinctly reported. This study aimed to address the connectivity between farming activities and malaria transmission. Methods The study took place in the agricultural setting of Nigeria Edu local government (9° N, 4.9° E) between March 2016 and December 2018. A pre-tested structured questionnaire was administered to obtain information on their occupation and malaria infection. Infection status was confirmed with blood film and microscopic diagnosis of Plasmodium falciparum was based on the presence of ring form or any other blood stages. Individuals who are either critically ill or lived in the community less than 3 months were excluded from the study. Results Of the 341 volunteers, 58.1% (52.9% in Shigo and 61.4% in Sista) were infected (parasitaemia density of 1243.7 parasites/μL blood). The prevalence and intensity of infection were higher among farmers (71.3%, 1922.9 parasites/μL blood, P = 0.005), particularly among rice farmers (2991.6 parasites/μL blood) compared to non-farmer participants. The occurrence and parasite density follow the same pattern for sex and age ( P < 0.05). Children in the age of 6 to 10 years (AOR: 2.168, CI: 1.63–2.19) and ≥ 11 years (AOR: 3.750, CI: 2.85–3.80) groups were two-and four-fold more likely to be infected with malaria. The analysis revealed that the proximity of bush and stagnant water to the farmer (73.9%, AOR: 3.242, CI: 2.57–3.61) and non-farmer (38.1%, AOR: 1.362, CI: 1.25–1.41) habitations influence malaria transmission. Conclusion This study highlights farming activities as a risk factor for malaria infection in agro-communities. Integrated malaria control measures in agricultural communities should therefore include water and environmental management practices.