There is a need to develop and adopt novel, more resilient, or “climate-smart” cropping strategies on the Canadian prairies, which are crucial for sustainable agroecosystem management. To examine how crop rotation influences soil organic matter and aggregate stability (AS) dynamics, six crop rotations: (i) conventional (control), (ii) pulse/oilseed intensified, (iii) diversified, (iv) market-driven, (v) high-risk and high-reward, and (vi) soil health-enhanced were established in 2018 at three field sites: Lethbridge, Alberta and Swift Current and Scott, Saskatchewan under no-till management. After 4-year, soil organic carbon (SOC), total nitrogen (TN), particulate organic matter carbon (POM-C) and nitrogen (POM-N), or mineral-associated organic matter C (MAOM-C) and N (MAOM-N) concentrations were not significantly affected by crop rotation in the 0–7.5 cm soil depth. However, crop rotation significantly altered AS at two of three sites, with both soil health-enhanced and high-risk and high-reward rotations having the highest AS at Lethbridge and Swift Current. Across all three sites, strong positive correlations were found among SOC, TN, MAOM, and AS. Moreover, MAOM-C and MAOM-N showed stronger relationships with AS than POM, perhaps suggesting a positive feedback loop on the stability of SOC and aggregation. Overall, the inclusion of pulses in rotations showed the potential to sustain soil quality, likely by offsetting low residue quantity with better residue quality and diversity, thereby supporting SOC accrual and AS similar to or greater than conventional cereal- or oilseed-dominated rotations.