Sustainable agriculture requires increasing farmers' knowledge of methods and fertilizers beneficial to soil and plant health. This study explored alternatives to chemical fertilizers to reduce their overuse and restore soil health. This study evaluated the effects of organic fertilizer and EM1 biofertilizer on the growth, yield, and chemical composition of two Zea mays Linnaeus, 1753 varieties, hybrid and local, under field conditions. Four fertilizer treatments were applied: organic fertilizer, EM1, organic + EM1, and a control. The results showed significant differences among treatments for most agronomic and biochemical traits. The combined organic + EM1 treatment produced the highest values for leaf number, ear diameter, and grains per row in both varieties. The hybrid variety exhibited superior vegetative growth, while the local variety responded better in grain protein and oil content. The highest protein content was observed in the local variety under the organic + EM1 treatment (9.08 g), followed by EM1 alone (9.02 g), while the control had the lowest value (8.38 g). Similarly, oil content was highest under the combined treatment, reaching 8–9%, compared with 5–6% in the control. These improvements are attributed to the positive effects of organic matter and EM1 biofertilizers in enhancing soil fertility, nutrient availability, and microbial activity. Overall, the findings indicate that using organic and EM1 fertilizers significantly enhances maize growth, productivity, and grain quality while promoting soil fertility and environmental sustainability. Therefore, reducing reliance on chemical fertilizers and replacing them with organic and bio-based alternatives represents a viable strategy for sustainable maize production and long-term ecological balance.