Abstract Background Malaria and soil-transmitted helminths (STH) represent significant public health challenges in tropical regions, particularly affecting children and impeding development. This study investigates the co-morbidity of malaria, caused by Plasmodium spp., and STH infections, including Ascaris lumbricoides(roundworm), Ancylostoma duodenale and Necator americanus (hookworm), and Trichuris trichiura(whipworm), in Nigeria. Methods We utilized malaria prevalence data from the Nigeria Malaria Indicators Survey (NMIS) for the years 2010 and 2015 and STH prevalence data from the Expanded Special Project for Elimination of Neglected Tropical Diseases (ESPEN) portal, covering the years 1978–2014. A Bayesian coregionalization model was employed to analyze the prevalence and incidence of malaria and STH, linking these data to climatic factors such as temperature and precipitation. The study’s findings highlight significant co-morbidity between malaria and STH, particularly in the southsouth and southeast regions. Results Our analysis reveals notable regional disparities: malaria prevalence is highest in the northwest and north-central regions, while Ascaris lumbricoides is widespread in both northern and southern states. Ancylostoma duodenale and Necator americanus(Hookworm) are predominantly found in the southwest, and Trichuris trichiura, though less prevalent, is significant in specific areas. Substantial co-morbidity between malaria and STH was observed, particularly in the South-South and southeast regions, indicating a compounded health burden. Furthermore, climatic factors significantly influence disease distribution; higher temperatures correlate with increased malaria prevalence, although temperature has a minimal effect on STH prevalence and incidence. In contrast, precipitation is positively associated with both malaria and STH incidence. Conclusions These findings enhance our understanding of the spatial distribution and risk factors associated with malaria and STH in Nigeria, providing vital insights for the development of public health policies and targeted intervention strategies.