Integrated biofertilizers such as Plant Growth-Promoting Rhizobacteria (PGPRs), cyanobacteria, and yeast can considerably improve the growth, integrity, and overall health of crops, including cowpea. In this study, we assess the benefits of applying microbial fertilizers as an eco-friendly approach to partially substitute chemical fertilizers while maintaining growth and yield characteristics in cowpea plants. We investigated the role of the three microorganisms, Bacillus amyloliquefacien (B), Nostoc mucorum (C), and Saccharomyces cerevisiae (Y), individually and in four possible combinations (B + C, B + Y, C + Y, and B + C + Y) as integrated bio-fertilizers on the microbial enzyme activities, plant growth parameters, and yield characteristics of cowpea. Plants inoculated with B + C + Y mixture resulted in significant improvement in dehydrogenase enzyme activity by 390%, chlorophyll by 180%, plant dry weight by 130%, and in the pod length and dry weight by 68% and 190%, respectively, compared to non-inoculated plants. The grain total carbohydrates increased by 170% over the control due to treatment with B + C + Y. The B + C + Y treatment also positively influenced the anatomy of the terminal leaflet with a 16.6% higher thickness of the midrib zone, 22.6% increase in vascular bundle length, and 42.4% and 33.5% increases in upper and lower epidermal leaf layers, respectively. Additionally, palisade and spongy tissues increased by 36.9% and 26.5%, respectively, compared to the control. An integrated nutrient management program using biofertilizers is recommended for achieving higher yields and environmentally safe cowpea production.