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• Wet aggregate stability was higher in soil health fields than conventional fields. • Soil properties were most responsive to the integration of soil health practices. • Less tillage with more cover crops was the most effective practices’ combination. • Site specific response varied based on soil texture and management practices. This study evaluated the effects of integrated soil health management in the US Upper Midwest over three years (2021–2023), under diverse cropping systems and soil textures. We assessed 15 field pairs, each consisting of one conventional (CV) and one soil health (SH) site, implementing contrasting management. Our analysis focused on four soil organic matter pools, six microbial indicators derived from phospholipid fatty acids (PLFA) and one physical indicator. Log response ratios (LRR) were calculated to compare pair-wise responses between medium and moderately fine-textured soils. Wet aggregate stability (WAS) showed consistent improvement; within each pair, more soil health based principles (reduced tillage, more cover crops and crop diversity) led to greater aggregate stability compared to the paired CV site. Medium-textured soils responded more strongly to soil health management than moderately fine-textured soils. To assess the effects of specific management practices, we built a mixed-effects model with practices and their interactions as fixed effects and soil health indicators as response variables. Results showed that most soil properties were significantly responsive to two management combinations, 1) tillage x cover crops, and 2) tillage x cover crops x crop diversity. Microbial indicators along with potentially mineralizable nitrogen (PMN) exhibited the strongest increases with integrated soil health management ( p < 0.05), followed by permanganate oxidizable carbon (POXC) and total N ( p < 0.1). Cover cropping alone moderately increased PMN ( p < 0.1). While site-specific behavior varied based on texture and management intensities, our overall results supported the adoption of integrated soil health practices for healthier agricultural soils.