Tomatoes are rich in lycopene, β-carotene, ascorbic acid and other mineral sources including phosphorus, potassium, zinc, magnesium and iron. Major constraints in tomato cultivation were high cost, poor cultivation due to adverse weather conditions, pest attacks, microbial infections and nutritional deficiency complications. Conventional fertilizers, pesticides, fungicides and growth regulators are effective at higher concentration, which induces specific toxic effects on soil fertility, plant yield and also affects the health status of humans, animals and soil associated microbes. The use of organic fertilizers to meet the soil nutrient demand increases the acidity of soil affecting plant growth, which turned the focus of researchers towards nanofertilizer. The present study focuses on synthesis of marine waste derived CaCO3 nanoparticles formulated with azadirachtin and panchakavya emulsion to develop a CaCO3 nanofertilizer. CaCO3 nanofertilizer developed through this study was investigated for its material properties and behavioral traits. Further, the in-vitro antifungal impact of the CaCO3 nanofertilizer was examined, and it was sprayed on tomato plants via foliar spray. CaCO3 nanofertilizer effectively inhibited fusarium wilt causing plant fungal pathogen and also exhibited enhanced growth and yield of tomatoes against pest attack and nutritional deficiency with effect to foliar treatment. Also, CaCO3 nanofertilizer enhanced the total carotenoid level and essential nutritional minerals in fruit yield of tomatoes. Overall, fabricated CaCO3 nanofertilizer exhibits synergistic role of fertilizer, pesticide, fungicide and growth regulator in tomato cultivation. It suggests that, CaCO3 nanofertilizer generated from renewable biowaste will become the innovative platform for sustainable agriculture.