Biodiesel, a renewable and biodegradable fuel derived from vegetable oils, is a promising alternative to petroleum diesel due to its lower greenhouse gas and pollutant emissions. Optimizing agricultural practices for feedstock production is essential to ensure high-quality biodiesel and reduced environmental impact. This study aimed to evaluate the effects of nitrogen fertilization and irrigation regimes on the fuel properties and engine emissions of biodiesel produced from winter rapeseed. A bifactorial field experiment was conducted in 2023-2024 in Aiton, Cluj County, Romania, on the winter variety ‘Dexter.’ Two irrigation regimes (non-irrigated, I₀; and irrigated at 50% of IUA, I₁) and four fertilization treatments (0, 100, 150, and 270 kg N/ha plus P and S) were tested in 10 m² plots. Irrigation was applied in autumn, spring, and summer, and nitrogen was split across three growth stages. Biodiesel was produced through methanol transesterification and analyzed for cetane number, sulfur content, and calorific value according to EN 14214 standards. Emissions (CO, HC, PM₁₀, NOₓ) were measured on a direct-injection diesel engine and compared to petroleum diesel. Biodiesel met EN 14214 standards, with favorable fuel properties. Compared to petroleum diesel, biodiesel reduced CO emissions by 34.5–39.5%, HC by 48.8–52.2%, and PM₁₀ by 42.3–46.9%, while NOₓ emissions increased slightly (2.5–9%). The best treatment combination was I₁ × N150, which resulted in optimal biodiesel quality and reduced emissions. Higher nitrogen rates (N270) increased NOₓ emissions, and irrigation consistently improved both biodiesel properties and emissions performance compared to non-irrigated variants. Proper nitrogen and water management in rapeseed cultivation can enhance biodiesel quality and reduce harmful emissions, contributing to climate-smart, zero-pollution agricultural practices. Further research is recommended to mitigate NOₓ emissions while maintaining fuel performance.