Maize grain hardness influences storage pest resistance, a key characteristic valued by smallholder farmers. The structural changes in the endosperm determine grain hardness and are influenced by agronomic practices. The purpose of this study was to establish whether supply of calcium and magnesium based fertilizers can alter physicochemical properties of local and hybrid maize varieties and reduce the infestation by larger grain borer (Prostephanus truncatus (Coleoptera: Bostrichidae)) during storage. Two local and one hybrid maize varieties commonly grown by smallholder farmers in Malawi were cultivated under three fertilizer treatments (NPK (nitrogen, phosphorous, potassium), NPK plus gypsum, and NPK plus dolomite). After harvest, the grains were classified into flint and dent types, followed by P. truncatus infestation and determination of their physicochemical properties. The addition of gypsum and dolomite fertilizers led to higher levels of amylose, total zein and β-14 zein, traits associated with kernel hardness, compared to the application of NPK fertilizer. Moreover, local maize varieties showed higher resistance to P. truncatus infestation, hardness and biochemical properties associated with hardness (total zein, α-19 and β-14 zein, starch lysophosphatidylcholine, and non-starch free fatty acid) compared to hybrid variety. Our study suggests the potential for utilizing Ca and Mg nutrition in maize to improve kernel hardness, thus adoption of gypsum and dolomite by smallholder farmers may be beneficial against P. truncatus during storage.