The influence of climate on soil microorganisms governs the input and output fluxes of carbon (C) from soils. The study of the drastic responses to drying-rewetting offers an opportunity to assess an aspect of ‘soil health’ via evaluating the role of microbes in soil biochemistry and C cycling. Recent evidence has consistently shown that communities exposed to extreme moisture fluctuations recurrently can better cope with the stress generated by them and exhibit a ‘resilient’ microbial response after rewetting (fast recovery of microbial communities to the pre-disturbance growth levels), whereas otherwise they show a more ‘sensitive’ response (slow recovery). However, it is still not known if land-use management can alter these responses. In this study, we investigated this issue by performing a drying-rewetting experiment on soil samples from two land-uses (permanent pastures and tilled croplands) and two depths (0–5 cm and 20–30 cm), and measured bacterial growth, fungal growth, and respiration at high temporal resolution. We then derived a series of indicators of soil health based on the characteristics of these microbial responses to drying-rewetting. Results showed categorically different patterns in soils from pastures and croplands, confirming the capacity of land use to change soil functioning. Tillage practices cancelled the stratification in the top 30 cm of soil and increased the exposure and adaptation of soil microorganisms to conditions of water stress, which caused shifts in the microbial responses to drying-rewetting. The sensitive patterns in bacterial growth found in undisturbed pastures were replaced by resilient responses in both shallow and deep croplands. Fungi showed a tendency for faster recoveries in croplands but patterns were consistently resilient in all sites and depths, indicating that fungi were little affected by land-use-induced disturbances. Respiration exhibited resilient-like responses in shallow samples, but in depth, they were sensitive in pastures and resilient in croplands. We also observed an alternated sequence of bacterial and fungal growth over time that suggested competition and different strategies of reactivation after rewetting by the two types of microorganisms.