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This study evaluated microbial communities of soil (0–10 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil type was an Olton sandy loam with an average of 16.4% clay, 67.6% sand and 0.65 g kg−1 of organic matter (OM). The cropping systems evaluated were grain sorghum (Sorghum bicolor L.)—cotton (Gossypium hirsutum) (Srg-Ct), cotton-winter rye (Secale cereale)-grain sorghum (Ct-Rye-Srg), and a rotation of forage (f) sorghum (Sorghum bicolor L. and Sorghum sudanense) with winter rye (Srf-Rye), which were under no-tillage (nt) and conventional tillage (ct) practices. Soil microbial communities under cotton based cropping systems (Srg-Ct and Ct-Rye-Srg) showed lower fungal:bacterial ratios compared to the soil under Srf-Rye. Soil under Srf-Rye showed higher population densities of Bacteroidetes and Proteobacteria while lower Actinobacteria compared to Srg-Ct and Ct-Rye-Srg. Chloroflexi, Gemmatimonadetes and Verrucomicrobiae were higher in tilled soil compared to the no-tilled plots. Regardless the limited irrigation available to sustain agricultural production within these dryland cropping systems, this study demonstrated that differences in microbial communities are more affected by crop rotation than tillage management history. Although soil fungal diversity was not analyzed in this study, pyrosequencing suggests that tillage practices can affect bacterial phyla distribution in this sandy soil.