Seventy composite samples of maize grains stored in five agro-ecological zones (AEZs) of Nigeria where maize is predominantly produced were evaluated for the presence of microbial metabolites with the LC-MS/MS technique. The possible relationships between the storage structures and levels of mycotoxin contamination were also evaluated. Sixty-two fungal and four bacterial metabolites were extracted from the grains, 54 of which have not been documented for maize in Nigeria. Aflatoxin B1 and fumonisin B1 were quantified in 67.1 and 92.9% of the grains, while 64.1 and 57.1% exceeded the European Union Commission maximum acceptable limit (MAL) for aflatoxin B1 and fumonisins, respectively. The concentration of deoxynivalenol was, however, below the MAL with occurrence levels of 100 and 10% for its masked metabolite, deoxynivalenol glucoside. The bacterial metabolites had low concentrations and were not a source of concern. The storage structures significantly correlated positively or negatively (p < 0.01 and p < 0.05), respectively with the levels of grain contamination. Consumption of maize grains, a staple Nigerian diet, may therefore expose the population to mycotoxin contamination. There is need for an immediate action plan for mycotoxin mitigation in Nigeria, especially in the Derived Savannah zone, in view of the economic and public health importance of the toxins.