Concern for food safety has continued to grow worldwide including the issue of mycotoxin contamination of food products from farm to fork. In this regard, soya bean seeds and processed soya bean powder bought from some Nigerian markets were screened for fungal and mycotoxin contamination. Fungal identification was done by both conventional and molecular methods after samples were cultured on potato dextrose agar (PDA), ohio agricultural experimental station agar (OAESA), malt extract agar (MEA) and czapek yeast agar (CYA). Mycotoxin analysis by thin layer chromatography and high performance liquid chromatography was done after extraction and clean-up by multi-mycotoxin extraction procedure and solid phase extraction (SPE) isolute strong ion exchange (SAX) columns. Results from the analysis showed that soya bean seeds had higher incidences of fungal species such as Alternaria (52.4%) and Aspergillus flavus (42.9%). Mycotoxins detected include aflatoxins, ochratoxin A and fumonisin B with highest concentration of 3.430 μg/g, 0.125 μg/g and 4.286 μg/g respectively, which were below regulatory limits. The study showed that there was co-occurrence of aflatoxins and fumonisin B1 in both sample types and though these values are low, should not be ignored as a result of health risks associated with exposure to these compounds.