Maize is a popular gluten-free grain, used in many dishes in Africa and elsewhere. It provides numerous nutrients (especially starch) and contains antinutritional factors (phytates). To reduce these factors and improve the nutritional and physical potential of maize, a number of treatments are required, including malting. This study therefore investigated the physicochemical, functional, structural, and pasting properties of two malted maize varieties (Atp-Y and Coca-sr) produce under optimal conditions. After receiving the two maize varieties from the Agricultural Research Institute for development, the Atp-Y variety was soaked for 30 h at 18.66 °C with 0.37% plant salt, followed by germination at 30 °C for 218.58 h and a ripening period of 40 h, while the Coca-sr variety was soaked for 3.90 h at 20.57 °C with 0.0219% plant salt, followed by germination at 30 °C for 251.55 h and a ripening period of 58.73 h. The flours obtained were subjected to physicochemical, structural, pasting and functional analysis. These analyses showed that the protein, fibre, ash, carbohydrate, starch and energy density content were significantly influenced by the variety. The Atp-Y variety had the highest contents of Ca (855.00 mg/100 g), Na (125.36 mg/100 g) and Cu (0.53 mg/100 g). The availability of Ca, Na and divalent cations was significantly higher in the Atp-Y variety. The Coca-sr variety contributed the most to achieving the protein (40.02 to 73.88%) and lipid (27.30 to 38.08%) requirements of children aged 0 to 59 months. The contents of phytates, cyanides and condensed tannins were similar in both varieties, while oxalates (7.88 mg/100 g), trypsin inhibitors (2.07 mg/100 g) and hydrolyzed tannins (15.02 mg EC/g) were more abundant in the Coca-sr variety. Phenols, flavonoids and saponins ranged between 45.96 and 68.39 mg GAE/g, 32.13 and 39.27 mg CE/g and 0.45 mg/100 g, respectively. No significant differences were found in the physical and functional properties, although the Atp-Y variety had a higher water retention and swelling capacity. Malting variety and conditions had no significant effect on Pasting Time, Setback, Setback ratio and Stability ratio in contrast to Pasting Temperature, Peak viscosity, Holding viscosity, Breakdown and Final viscosity. The Atp-Y grade exhibited the highest pasting parameters when pasting temperature was excluded. Scanning electron microscopy showed that the microscopic structure varied from one variety to another, although the grains had similar sizes. The Microscopic dispersions of grains testifies to the enzymatic activity in the Coca-sr variety, the compact surface layer with protruding grains testifies to the fiber richness of the Atp-Y variety. The grain distribution of the particles showed that more than 50% of the grains in both types were 400 µm in size. X-ray diffraction (XRD) showed that the degradation of the crystalline structure of the starch depended on the variety and the physiological phenomena taking place there. These results clearly show that these flours are well suited for the formulation of foods with high energy and nutritional value. However, they could also be used as sweeteners in panification or as raw materials in the brewing industry.