The excessive application of mineral fertilizers in maize cultivation leads to progressive soil contamination in the long term and increases the cost of production. An alternative to reduce over-fertilization is to perform a partial replacement with microbes that promote nutrition and growth, such as Arbuscular Mycorrhizal Fungi (AMF). A pot experiment which was followed by two field experiments was performed with and without the application of indigenous AMF in combination with five nitrogen–phosphorus–potassium (NPK) fertilization rates (100% NPK = N120P60K60; 75% NPK = N90P45K45; 50% NPK = N60P30K30; 25% NPK = N30P15K15; control = N0P0K0). The objective was to investigate whether the soil application of indigenous mycorrhizal fungi inoculum combined with NPK fertilization can provide higher maize yields and soil-available N, P, and K than chemical fertilization can alone. The greenhouse results showed that the application of AMF with a 50% NPK treatment significantly increased the plant’s growth, root colonization, leaf chlorophyll content, and N, P, and K tissue content. The results from the field conditions showed that there was a highly significant yield after the treatment with AMF + 50% NPK. The study also revealed that mycorrhizal fungi inoculation increased the available soil N and P concentrations when it was combined with a 50% NPK dose. This suggests that the inoculation of fields with AM fungi can reduce the chemical fertilizer application by half, while improving soil chemistry. The results suggested that AMF inoculation can be used in integrated soil fertility management strategies.