Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou’s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.