To assess digestate’s efficacy as a fertilizer for basil development, a two-year pot experiment was established, comprising four fertilization treatments: chemical fertilizer (F), digestate (D), combined chemical fertilizer and digestate (1:1, FD), and unfertilized control (C). Key metrics assessed included: plant height, chlorophyll concentration index (CCI), total biomass (TB), leaf production (LP), essential oil yield, and composition. Post-harvest soil analysis evaluated nutrient and heavy metal content and pathogen contamination in soil and leaves. FD treatment produced the highest TB (68.2 g plant⁻¹) and LP (52.7 g plant⁻¹). Digestate application substantially enhanced substrate nutrient availability, increasing extractable phosphorus by 68.5%, potassium by 134.4%, and organic matter by 54.7%. Essential oil yield was significantly higher in the control plants. Notably, different fertilization regimes altered secondary metabolite synthesis. Specifically, fertilization with digestate favored sesquiterpenes synthesis, inorganic fertilization enhanced methyleugenol and β-farnesene synthesis, while the control showed higher limonene, eugenol, and linalool. Heavy metal accumulation in the soil was negligible, remaining well within regulatory limits. Salmonella spp. were not detected. Pathogen concentration in the soil was low, while Enterococcus faecalis were marginally below EU safety limits (100 cfu g⁻1) on the leaves.