Land use and farming practices significantly influence soil health. This three-year study evaluated the effects of transitioning from conventional tillage (CT) to conservation agriculture (CA) on soil properties and fauna communities in vegetable production systems in Battambang (clay loam) and Siem Reap (sandy loam), Cambodia. Soil samples (0–20¿cm) were analyzed for physicochemical properties, soil macro- and meso-fauna abundance, richness, and diversity. CA significantly improved soil fertility, increasing nitrogen (N), phosphorus (P) and soil organic carbon. Soil mesofauna abundance, richness, and diversity increased under CA, particularly in Battambang, with Entomobryomorpha, Poduromorpha, Symphypleona and Diptera showing greater abundance. While CA had positive effects in Siem Reap, the improvement was less pronounced. Soil mesofauna response to CA varied by soil type, with clay loam soils exhibiting a greater positive response than sandy loam. These findings emphasize the significance of soil type in optimizing CA practices to improve soil health and mesofauna communities in these agroecological conditions.