Protected cultivation of high-value crops such as tomato, with several health benefits, is gaining global significance. This study explored the influence of aqueous formulations of cyanobacteria-Anabaena laxa (C11), Nostoc carneum (BF2), and Anabaena doliolum (BF4), applied as soil drench at pre-flowering and fruiting stages, on the dynamics of soil and plant attributes important for growth, productivity, and quality of fruits in an indeterminate tomato variety (NS4266) under protected cultivation. Drenching with the BF2 formulation resulted in a significant fold-increase in soil dehydrogenase activity and an increase of 40–45% in soil nitrogen availability; positively impacted glutamine synthetase activity, fruit weight, lycopene content, skin elasticity, in comparison to control. C11 drenching led to a 17% elevation in soil microbial biomass carbon, besides bringing about a 24 and 54% enhancement in available phosphorus and iron content. Additionally, it also enhanced chlorophyll a, b and total pigments by 54–65% over control. Principal Component Analysis (PCA) and Multivariate analysis showcased the distinct effects of cyanobacterial formulations on crop growth and soil fertility, as well as the significant and positive correlations among quality, plant, soil, and yield attributes contributed through cyanobacterial drenching. This investigation highlighted cyanobacterial drench as a promising organic option to augment soil nutrient availability, bolster overall productivity, and enhance fruit quality in tomato grown under protected cultivation.