Assessment tools are needed to evaluate the effect of farming practices on soil health, as there is increasing interest from growers to improve the health of their soils. However, there is limited information on the efficacy of different soil health indicators on commercial farms and perhaps less so on organic farms. To assess efficacy, three organic growers in cooperation with the Ecological Farmers Association of Ontario’s Farmer-Led Research Program tested management sensitivity, measurement repeatability, and consistency of interpretation of different soil health indicators. On each farm, we compared permanganate-oxidizable carbon (active carbon), organic matter, wet aggregate stability, phospholipid fatty acid analysis, Haney soil health test, and Haney nutrient test on one field of grower-perceived high productivity, one field of grower-perceived low productivity, and one reference site (undisturbed, permanent cover). Our results were consistent with previous research that showed grower perception of productivity and soil health associated with management-sensitive soil health indicators. Of the indicators tested, active carbon was the only indicator that was sensitive, repeatable, and consistent across the three farms, and soil organic matter was highly repeatable and consistent to detect differences greater than 0.5% organic matter. This study highlights differences among soil health indicators on commercial farms, and it concludes that active carbon and organic matter were the most useful soil health indicators for these organic farms. Participating growers intend to use results to benchmark current soil status and to help guide land management decisions towards improved soil health.