While soil microbial community shifts can widely affect SOM decomposition, nutrient re-cycle and biogeochemical outputs, the temporal dynamics of the microbial ecological succession in natural soils is far from being understood. This is particularly relevant in karst ecosystems, where shallow lepotsoils, with rapid drainage, meteorological pulses and microclimatic variability can expose microbial communities to abrupt environmental changes. By a nested random sampling design, we collected topsoil samples from three plots at two two temporal scales: a short-term survey, with sampling every two days over a month, and a medium-term survey sampling every two-weeks from beginning of April to mid of October. Bacterial and fungal communities were reconstructed from eDNA extracted from the soil samples through metabarcoding targeting 16S rRNA V3–V4 and ITS1 markers, respectively. Soil chemical-physical properties including texture, pH, organic C and total N percent content, and bulk density, were assessed by standard protocols, while soil water content and temperature were continuously monitored throughout the sampling campaign. Both bacterial and fungal communities showed marked variability in taxonomic diversity and composition and over time, with remarkable changes occurring not only across the seasonal gradient but also over short-time intervals of few days. Alpha diversity varied significantly through time for both marker datasets, clearly indicating that microbial diversity in karst soil is highly dynamic, following shifts in environmental regimes, even within short temporal windows. When exploring the same relationships using the functional annotation of bacteria and fungi datasets as available form public web platforms (i.e. FAPROTAX, FUNGuilds) a clear association of microbial successional dynamics with microclimatic dynamics emerged, with interesting implications for topsoil organic C shifts. These results, highlighting karst soils as dynamic microbial habitats, clarify that soil microbial succession follows a peculiar dynamic, over timescales completely different from those occurring for soil fauna or plant communities. As such, it can also decisively affect our perception of soil biological quality and biodiversity according to the time of sampling.