Forest soil biodiversity, which drives natural ecosystem multifunctionality, can be altered by incorrect forestry management practices. Pinus laricio is the most representative and widespread conifer species in Calabria, South Italy, and appropriate management is needed to maintain Pinus laricio forest for its great economic and natural value. In Europe, thinning is considered the most effective silvicultural treatment to maintain/increase the ecological value of coniferous stands. In this study, moderate thinning (MT), intense thinning (HT), and clear cut (CC) treatments were used to manage Pinus laricio stands with the aim of identifying the thinning intensity that is less detrimental to soil biodiversity. The effects of the different thinning intensities were evaluated, in two contrasting seasons (summer and winter), on the abundance, and diversity of arthropods, fungi, and bacteria colonies as well as on selected soil properties (organic matter, humification index, bulk density, pH) related to soil habitability. Results evidenced that the abundance, species richness, and diversity of arthropods, as well as fungi, bacteria colonies, and soil properties, changed with the treatments and seasons. Under HT, the greatest biodiversity and the highest amounts of arthropods, fungi, and bacteria were found in both seasons. This study finds evidence for Connell’s intermediate disturbance hypothesis, highlighting that the greatest organic carbon content and humification index, as well as the lowest bulk density, found in HT reduced the likelihood of competitive exclusion between occurring species, thereby promoting high species richness and diversity. This study gives insights into ecological relationships between understory composition related to tree species abundance and soil community.