Humans started using soil for agriculture around 23,000 years ago and today soils provide us with 95% of our food. However, because of soil degradation and urbanization, the amount of soil available to meet human demands is decreasing. Soil quality can be improved through management and is determined by soil properties like structure, organic matter (OM) content, water stability of aggregates, pH, and hydraulic properties. After the green revolution in the 1960s new crop cultivars were bred and sown aiming higher crop yields. Modern and older bred Zea mays (maize) genotypes may also differ in microorganism recruitment, root growth, and plant biomass, which are factors that can be related to soil quality and the sustainability of the agricultural systems. The objective of this study was to determine whether different maize breeding origins and inoculation with Rhizophagus irregularis and Azospirillum brasilense in an artificial soil influenced shoot biomass and soil parameters, including soil aggregates (size and water stability), water repellency (WR), water holding capacity (WHC), and pH. The experiment followed a factorial design with three maize breeding origins: modern Brazilian hybrids (MBH), modern German hybrids (MGH), and old maize cultivars (OMC) before the green revolution, and two treatments: one inoculated with microorganisms and one non-inoculated treatment. The aggregate size distribution (ASD) was determined by the size fractions 0–250 µm, 250–500 µm, 500 µm–1 mm, 1–2 mm, and 2–4 mm by dry sieving. The percentage of water-stable aggregates (WSA) was determined for aggregates with a diameter of 250 µm–1 mm and 1–4 mm by wet sieving. WR of the soils was examined by the water infiltration method. Shoot biomass, WHC, and pH of the soils were also evaluated. Older cultivars had fewer aggregates with a diameter of 0–250 µm, more WSA with a diameter of 250 µm–1 mm, less WSA with a diameter of 1–4 mm, and less shoot biomass compared to modern cultivars. Inoculated modern cultivars showed a decrease in WSA (1–4 mm) and an increase in shoot biomass, whereas older cultivars were not affected by inoculation. The hydraulic properties and pH showed no differences between modern and older cultivars. In conclusion, it was demonstrated that the percentage of aggregates with a diameter of 0–250 µm, the percentage of WSA (250 µm–1 mm and 1–4 mm), and shoot biomass differed between modern and older cultivars. Also, they responded differently to inoculation with A. brasilense and R. irregularis regarding the amount of WSA with a diameter of 1–4 mm and shoot biomass. It could be suggested that these differences are due to different exudates of modern and older cultivars and their subsequent interactions with the microorganisms. The exudates and their interactions with the microorganisms should be investigated in future studies. So, this knowledge could be a guide for plant breeding, with the aim to improve the soil structure in agricultural fields.