<p>The global demand for sustainable and eco-friendly alternatives to traditional silica nanoparticle (SiNP) synthesis has stimulated research interest in the biogenic routes, utilizing agricultural waste. This study investigates an innovative fungal-mediated biotransformation of sugarcane bagasse into SiNPs using <i>Aspergillus niger</i> MSF3. Fungal incubation of bagasse led to a silica release of 217 mg/L by 14th day, confirming the inherent silica bioavailability in substrate and its suitability for microbial valorization. To further enhance the process efficiency, various process parameters were optimized using the Central Composite Design (CCD)-based RSM. The model was statistically significant (<i>p</i> &lt; 0.0001, R² = 0.9990). Temperature and substrate concentration were shown to have the most influence on fungal growth and subsequent release of soluble silica from the agro-waste. Under optimized conditions, the silica yield increased to 269.66 mg/L, compared to that obtained under non-optimized conditions. Furthermore, an economic assessment revealed that the production cost for 1kg of biogenic SiNPs was approximately 66% lower than the market price of commercially available SiNPs, thereby confirming the economic feasibility of utilizing bagasse as a sustainable feedstock for SiNP synthesis. This study presents a scientifically validated, low-cost, and sustainable platform for SiNP production from sugarcane bagasse, thus eliminating the need for corrosive acids and energy-intensive pretreatment. This further contributes directly to the principles of green chemistry, waste valorization, and circular economy. The developed process aligns with the United Nations Sustainable Development Goals, particularly SDG 9 and SDG 12, by promoting innovative, resource-efficient manufacturing strategies that support sustainable industrial development.</p> Graphical Abstract <p></p>