The European beech (Fagus sylvatica L.) is a dominant tree species in European forests and it has a huge ecological significance and high economic value. Due to its large dimensions, it can produce large amounts of decayed wood (CWD) which may be critical for maintaining the population of many rare species including mites. Many studies focused on mite (Mesostigmata) abundance, species richness, or diversity in CWD, however, our knowledge on mite biomass is still scarce. Therefore, the main aim of that study was to recognize the Mesostigmata biomass in logs and adjacent soil. In total, 90 samples (125 cm³, 5 cm depth) were collected from European beech logs and soil with litter thickness. Soil samples were collected from ecotone zone (soil near the log) and further three distances—0.5 m, 1.0 m, 1.5 m away from the log. Body length and width were measured for each individual of rare species and in the case of common species at least for 10 individuals. Our study revealed the highest mite biomass in CWD and soil near to the log (ecotone). Total male biomass was the highest in CWD and differed significantly from all other soil microhabitats. Female biomass did not differ between soil and CWD, whereas deutonymphs biomass differed between CWD and soil 1.0 m away from the log. Mean abundance, species richness, and diversity did not differ between the microhabitats. Decaying logs were dominated by Janietella pulchella whereas soil by Veigaia nemorensis. In conclusion, decayed European beech logs maintain the highest male and deutonymph biomass when compared to adjacent soil. Beech logs are important microhabitats for Mesostigmata mite communities, where they reached the highest abundance.