The global crises of biodiversity loss and land degradation have intensified the need for effective restoration strategies. In Portugal's Serra da Arrábida Natural Park, which showcases some of Europe's best-preserved Mediterranean vegetation, a limestone quarry owned by SECIL has been the focus of both natural and artificial restoration efforts. These efforts, which began in 1983 and continued through 2010, aimed to restore the quarry site using the surrounding ecosystem as a blueprint. While the vegetation recovery has been well-studied, how soil microbiota—crucial players in ecosystem health—respond to such restoration remains less explored. In our study, we combined physicochemical soil analyses with high-throughput sequencing of the bacterial 16S rRNA gene and the fungal ITS2 region to investigate these microbial communities. By sampling soils at intervals representing approximately 10 years post-revegetation, we created a chronological sequence to track how the microbiome changes over time. Our results revealed that microbial communities in different geological zones—limestone versus marlstone—were distinctly shaped by the restoration techniques applied. The time elapsed since restoration was a key factor influencing these microbial assemblages. We observed significant variability in bacterial functions within each restored zone, while fungal functions showed notable differences across zones. Interestingly, areas that were more recently restored harboured higher levels of plant pathogens, whereas zones that had undergone long-term restoration displayed microbial functions more closely aligned with those of native vegetation. This research sheds light on the dynamic responses of soil microbiota to revegetation and underscores the importance of considering microbial communities in restoration projects. The findings also point to areas where further research is needed to fully understand the intricate relationships between soil health, microbial communities, and ecosystem recovery.