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Soil mesofauna play an essential role in soil functioning. However, in studies on the impact of agricultural management on soil quality, the overall abundance of soil mesofauna and specific groups thereof has not been widely used as an indicator in developing countries. Here, we used soil mesofauna as a soil quality indicator compared to more traditional soil chemical, physical, and microbial indicators, in a comparison of the impact of three diverse agricultural management systems in Central Cuba: state (CSt), conventional private (CPr), and organic private (OPr) farms. We sampled the top 20 cm of soil of 30 fields from 12 farms and 1 natural reference site (NR) and analysed a number of soil chemical, physical, and microbial soil parameters as well as mesofauna (Acari and Collembola, further subdivided into Mesostigmata–Prostigmata–Oribatida–Astigmata and Isotomidae–Entomobryidae, respectively). Differences in soil properties between agricultural fields and natural soil were observed (especially in the multivariate analysis), but no significant differences were observed between agricultural systems, probably due to a lack of differences in soil organic carbon (SOC) content. The mesofauna differed strongly between the NR and the two conventional management practices (CSt and CPr), both in total numbers and in group numbers for most groups and in both rainy and dry seasons, whereas there were almost no significant differences between NR and OPr. Principal component analysis based on mesofauna clearly distinguished NR from all farming systems and OPr from CSt and CPr. Differences in soil mesofauna were mainly attributed to the use of synthetic pesticides. We conclude that in this context, without clear differences in SOC content between agricultural fields, mesofauna is a superior soil quality indicator. Our results indicate that simple counts of total abundance are as useful as counts of specific mesofauna groups irrespective of the sampling period (dry or wet season). [ABSTRACT FROM AUTHOR]