This investigation was carried out to assess the bacteria associated with cocoa beans at different stages of fermentation and determine the changes in the phytochemical constituents of the fermenting beans. The pour plate technique was used for bacterial isolation while phytochemicals were assessed based on standard qualitative chemical reactions. The total bacterial count on the cocoa beans reduced during fermentation from the initial 86.2±0.02 x 105 CFU/g (day 0) to 1.00±0.00 x 105 CFU/g on day 5. However, there was an increase in the lactic acid bacteria count from 48.7±0.03 x 105 CFU/g (day 0) to 111.7±0.03 x 105 CFU/g on day 3, then reduced to 51.4±0.01 x 105 CFU/g on day 5. Staphylococcus aureus, Micrococcus luteus, Bacillus subtilis, Lactobacillus fermentum, Lactobacillus plantarum and Lactobacillus acidophilus were isolated from the cocoa beans at different stages of the fermentation. There was a gradual increase in the temperature of the fermenting cocoa mass from the initial 25.6°C recorded at the beginning of the fermentation to 42.8°C recorded on day 5. Also, the pH of the fermenting cocoa beans reduced significantly from 6.1 at the commencement of the fermentation to 3.2 on day 5. In the total titratable acidity assay, the acidity of the cocoa beans increased from 3.12% at the beginning of the fermentation to 7.12% on day 5. Further, in the phytochemical screening, only alkaloids, phenols, steroids and flavonoids were detected in the beans throughout fermentation period whereas tannin and saponin were not found in the beans at any stage of fermentation. The preset phytochemicals got reduced in intensity as fermentation advanced. From these results, it can therefore be concluded that fermentation helps to improve the taste quality and phytochemical properties of Nigerian cocoa beans.