Integrated crop and livestock systems (ICLS) have the potential to minimize soil degradation, improve soil health, and maximize food production. Our goal was to evaluate the impact of no-till (NT) in association with ICLS on soil health and soybean yield in Inceptisol and Oxisol soils in Southern Brazil. The response of physical, chemical, and biological soil health indicators to soil and crop management systems was measured over the short- (<5 years) and long-term (>10 years) under ICLS with soybean in spring/summer and forage grazed by cattle in the autumn/winter. A soil management index was calculated for each soil based on ICLS management. Independent of soil type, ICLS in association with NT for 10+ years improved chemical and biological properties in the near soil surface (0–6 cm depth). The Soil Management Assessment Framework (SMAF) scores for soil organic carbon (SOC), phosphorus (P), and bulk density were close to 1.0 in the Inceptisol, independent of management or soil depth, while the pH scores were lower in the ICLS topsoil. For the Oxisol, the SMAF scores for SOC and P were approximately 1.0 in the 0–6 cm depth under long-term ICLS. The SMAF overall soil quality index was high (approximately 0.9) for both soils and there were no significant differences between management practices. Overall, the adoption of ICLS in association with NT (i) improved or maintained soil health, (ii) promoted soil carbon sequestration, and (iii) increased soybean yield in the studied soils. This study confirmed the potential for conservation practices (ICLS combined with NT) to improve soil quality with environmental sustainability.