Container-grown geranium (Pelargonium hortorum) may experience delayed flowering and leaf chlorosis due to limited nutrient availability and a high carbon-to-nitrogen ratio in the growing medium. Optimizing substrate composition together with biostimulant application may therefore improve both flowering performance and ornamental quality. However, the interactive effects of eco-enzyme application and organic growing media formulation on geranium flowering remain unexplored. This study assessed the interactive effects of eco-enzyme concentration and organic growing media composition on the flowering performance of geranium. A factorial randomized block design was used, evaluating three eco-enzyme concentrations (0, 15, and 30 mL L⁻¹) and three media formulations composed of cocopeat, manure, and rice husk biochar (1:1:0, 1:1:1, and 1:1:2). The M2 medium (1:1:1) was well balanced, with favorable bulk density, porosity, and water-holding capacity that supported root development and nutrient uptake. Eco-enzyme application at 15–30 mL L⁻¹ significantly (P < 0.05) increased flower cluster number by 31.1–59.0% in the M2 medium compared to untreated plants. The M2 medium increased flower number and cluster diameter by 18.9% and 6.3%, respectively, compared to the M3 (1:1:2) formulation, while 30 mL L⁻¹ eco-enzyme increased flower number by 25.8% compared to the control. These combined effects promoted earlier, fuller flowering and greater plant vigor. Incorporating eco-enzyme biostimulant application with an optimized organic substrate therefore offers a practical and sustainable strategy to enhance geranium flowering performance and ornamental quality.