This study concerned the effect of different intercropping systems (alternating rows and alternating strips) of maize and soybean compared with single cropping, in combination with different fertilisers (biofertiliser, organic fertiliser, and urea) on the potential availability of magnesium (Mg), iron (Fe) and zinc (Zn) from grain, through their ratio with phytate (as inhibitor) and β-carotene (as promoter). The higher grain yield and land equivalent ratio obtained under alternating rows   biofertiliser treatment demonstrated the improved ability of crops in close proximity for better utilisation of existing agro-ecological conditions. Alternating rows   organic fertiliser decreased the molar ratios phytate : β-carotene, phytate : Fe, phytate : Mg and phytate : Zn, indicating increased availability of the mineral elements in both crops. However, alternating strips   organic fertiliser contributed mostly to an increase in β-carotene, Mg, Fe and Zn concentrations in soybean. Increased grain yield of both crops was followed by decrease in β-carotene and increase in phytate, particularly in maize. In soybean, β-carotene could be considered as the main contributor to Fe availability. Accordingly, cropping in alternating rows or strips, combined with biofertilisers, could serve as fortification measures for improved nutritional quality of maize and soybean grain, without grain yield losses.