Biological products used in soybean seed treatment can enhance soil microbial activity, thereby improving soil health. Brazil is the world‘s largest producer of soybeans and has a vast and diverse cultivation area characterized by varying weather and soil conditions. However, there is a lack of studies that have assessed the soil health response to soil biological conditioners based on calcium sulfate dihydrate applied by seed treatment at large-scale farmer-led and over extended periods in Brazilian soybean fields. To address this gap, we carried out a large-scale farmer-led study across a 3000-km transect to evaluate the soil health responses to a biological conditioner over three consecutive years. Soil health indicators including soil organic carbon, extracellular ß-glucosidase enzyme activity, soil bulk density, soil pH, available phosphorus, and exchangeable potassium were measured, interpreted, and integrated into a soil health index (SMAF-SHI) to compare experimental strips with and without of the soil biological conditioner. A dataset of 87 sampling points collected from 15 farmer-led experiments over three consecutive years of the soil biological conditioner application (i.e., 2021 corresponds to one application, 2022 to two applications, and 2023 to three applications) was analyzed. The results showed site- and year-specific alterations on soil chemical, physical, and biological indicators, as well as overall SMAF-SHI. In general, the effects of the soil biological conditioner application were subtle and statistically undetectable for most of the metrics over three consecutive years of application. However, we observed potential changes in soil organic carbon, extracellular β-glucosidase enzyme activity, and soil bulk density indicators after two and three years of the soil biological conditioner application. To further understand the long-term effects of biological conditioners on soil, we propose continued soil health monitoring over time, with a particular focus on the rhizosphere, and the inclusion of molecular biology methods to measure the abundance, diversity and functionality of the soil microbiome.