Soil-plant interactions of different wheat species (e.g., common, synthetic, durum and wild emmer ancestor) have not been studied yet. Therefore, our study was conducted to examine the interactive effect of 39 treatments including four wheat species (twelve varieties) and three soil types (loamy sand, sandy loam and sandy clay loam) on soil physical and biophysical quality indicators in a greenhouse pot experiment. The rhizosphere data were compared with the no plant (control) soil as well. The results revealed that the rhizosphere soils had a greater soil organic carbon (SOC) storage compared to the no plant soil, with the synthetic wheat species possessing the highest SOC content (order of SOC: synthetic > durum > emmer > common > control). The highest and the lowest SOC values (0.79 and 0.69 kg 100 kg−1) were observed in the rhizosphere of synthetic wheat S88 and common wheat CK varieties, respectively. The SOC showed a positive correlation with root morphological traits such as root volume and root dry weight. Basal soil respiration (BSR) showed significant variation among the four wheat species, and common and emmer ones had the highest BSR values. The maximum and minimum values of BSR (21.9 and 10.9 mg CO2 kg−1 soil day−1) were observed in the rhizosphere of the common species planted in sandy loam soil and in the loamy sand bulk soil (control), respectively. The presence of plant roots significantly increased BSR compared to the control (bulk soil); on average, the BSR in the rhizosphere was 21% greater than the control. Both the wheat species and soil type significantly affected the soil water repellency index (RI) and wettability parameters, but the interactive effects of treatments (i.e., wheat species and soil type) were not significant. The soils in all of the studied treatments were sub-critically or slightly water repellent (i.e., contact angle lower than 90°). The RI values were measured in the order emmer > durum > common > control ≥ synthetic; however, the difference between the synthetic species and bulk soil was not significant. Plant roots increased the soil hydrophobicity by increasing the SOC storage and significant variations in RI among the wheat species indicated that the emmer, durum and common species with greater RI might have better soil physical quality in the rhizosphere. The wheat plants substantially increased water-stable aggregates and decreased water-dispersible clay in the rhizosphere compared to the bulk soil. These findings showed that wheat roots were able to alter the structural stability of the rhizosphere soil. Correlation analysis indicated that soil structural stability was closely related to the SOC, microbial activity, water repellency and root morphological traits. Principal component analysis was used to enhance visualization, identify interrelationships between soil quality indicators and categorize wheat varieties.