Fermented maize dough meals form a large proportion of people's diet in Ghana. To enhance the nutritive value of these carbohydrate-rich foods, protein complementation was introduced. In this study, microbial ecology of fermenting maize dough fortified with 20% cowpea was investigated. A total of 106 microbial strains were isolated from different batches of the fermenting dough at periodic intervals. Ten genera of microorganisms namely Lactobacillus, Leuconostoc, Saccharomyces, Debaryomyces, Candida, Bacillus, Micrococcus, Klebsiella, Escherichia and Aspergillus were identified, with lactic acid bacteria species being predominant. A lactic count of log 9.9 cfu/g was obtained at the end of 72 h fermentation relative to log 6.6 cfu/g recorded for aerobic mesophiles. At the 12 h fermentation period, the population of yeasts was less than log 1.0 cfu/g, but gradually rose to log 5.36 cfu/g by 48 h followed a slight decline at the end of 72 h fermentation period (log 4.08 cfu/g). Enteric microorganisms that were isolated from the raw cowpea were less than log 1.0 cfu/g at 12 h of fermentation, while the Aspergillus species were isolated from the raw maize and the dough subjected to drying treatment. The growth of inoculated enteropathogenic E. coli and S. typhimurium was inhibited in the cooked, fermented maize-cowpea dough, and at 72 h, they were not within detectable limit. The study concluded that addition of cowpea at 20% level did not affect the natural fermentation characteristics of the maize dough.