Recent advances in multispectral imaging-based technology have provided useful information on seed health in order to optimize the quality control process. In this study, we verified the efficiency of multispectral imaging (MSI) combined with statistical models to assess the cowpea seed health and differentiate seeds carrying different fungal species. Seeds were artificially inoculated with Fusarium pallidoroseum, Rhizoctonia solani and Aspergillus sp. Multispectral images were acquired at 19 wavelengths (365 to 970 nm) from inoculated seeds and freeze-killed ‘incubated’ seeds. Statistical models based on linear discriminant analysis (LDA) were developed using reflectance, color and texture features of the seed images. Results demonstrated that the LDA-based models were efficient in detecting and identifying different species of fungi in cowpea seeds. The model showed above 92% accuracy before incubation and 99% after incubation, indicating that the MSI technique in combination with statistical models can be a useful tool for evaluating the health status of cowpea seeds. Our findings can be a guide for the development of in-depth studies with more cultivars and fungal species, isolated and in association, for the successful application of MSI in the routine health inspection of cowpea seeds and other important legumes.