An indicator which will be used to monitor whether a management practice is improving soil health must be sensitive to management changes. However, it should not be overly influenced by variations in sampling time or location, previous crop, or annual differences in weather or operations timing. In this study, we assessed the sensitivity and variability of several soil health indicators in long-term plots under typical farming practices in a Mediterranean climate. These plots have been conventionally or organically farmed in a corn (Zea mays L.)-processing tomato (Solanum lycopersicum L.) rotation for 25 years. We sampled in both crop phases prior to planting and midseason for two consecutive years, analyzing subsamples taken from three adjacent locations per plot. Management was the most significant factor differentiating most indicators, particularly indicators of biological processes and carbon accumulation. While management differences were consistent across sampling times, average indicator values for a management system often varied significantly between dates and years. Crop phases, conversely, were usually similar. Accounting for soil texture increased management sensitivity for aggregate stability and most carbon accumulation indicators. Sensitive indicators such as mineral N, particulate organic matter carbon and mineralizable carbon had greater subsample variability than indicators measuring large, stable pools, like total carbon. Our results show that indicators relating to organic carbon and biological processes This article is protected by copyright. All rights reserved. most strongly differentiated the two systems, and underline the importance of using consistent sampling dates. They also suggest that an indicator dataset including both stable and sensitive indicators may be the most reliable to interpret.