Biofertilisers harbouring living organisms hold allure due to their prospective favourable influence on plant growth, coupled with a diminished environmental footprint and cost-effectiveness in contrast to conventional mineral fertilisers. The purpose of the present study was to evaluate the capacity of a specific microalga (MACC-612, Nostoc linckia) biomass and plant growth-promoting bacteria (PGPB) separately and together to improve crop growth and promote soil health. The research used a factorial design within a completely randomised block framework, featuring four replications for three consecutive years across different fields. The experiment utilised three levels of microalga (control, 0.3 g/L of N. linckia, MACC-612, and 1 g/L of N. linckia, MACC-612) and three levels of bacterial strains (control, Azospirillum lipoferum and Pseudomonas fluorescens). The result demonstrated that the use of N. linckia and PGPB separately or jointly as soil treatment resulted in a substantial improvement in chlorophyll, plant biomass, soil humus, and nitrogen, depending on the environmental conditions of the years. The combined use of N. linckia and PGPB results in an improvement in dry leaf weight by 35.6–107.3% at 50 days after sowing (DAS) and 29.6–49.8% at 65 DAS, compared to the control group. Furthermore, the studies show that the synergistic application of N. linckia at 0.3 g/L, in conjunction with A. lipoferum, significantly improved total nitrogen and (NO3− + NO2−)-nitrogen, registering increases of 20.7–40% and 27.1–59.2%, respectively, during the study period. The most effective synergistic combination was identified through the application of 0.3 g/L of N. linckia along with A. lipoferum. Hence, application of biofertilisers through synergistic combinations of two or more microorganisms, such as microalgae and bacteria, holds promise in improving crop chlorophyll, growth, and soil nitrogen.