Afforestation is widely used to restore degraded Mediterranean landscapes, yet restoration success is often evaluated using vegetation establishment or soil carbon accumulation, with less attention to belowground ecosystem functioning. We assessed whether Cedrus libani afforestation promotes soil functional recovery in degraded Mediterranean karst and whether structural and microbial indicators provide robust measures of restoration progress under edaphic heterogeneity. Topsoil (0–10 cm) was sampled from degraded non-afforested reference land and 10-, 15-, and 25-year-old plantations in southern Türkiye. Soil organic carbon (SOC), total nitrogen (TN), aggregate stability, microbial biomass carbon (MBC), basal respiration, microbial quotient (qMic), and metabolic quotient (qCO₂) were determined. Afforested soils had higher SOC (1.55% vs. 2.37–3.35%), TN (0.053% vs. 0.087–0.190%), aggregate stability (61.3% vs. 77.8–84.9%), and MBC (180 vs. 288–536 µg g⁻¹), whereas basal respiration declined from 0.96 to 0.30–0.36 µg CO₂–C g⁻¹ h⁻¹ and qCO₂ from 5.41 to 0.54–1.39. qMic did not differ significantly among chronosequence classes. MBC was strongly associated with SOC (ρ = 0.917, P < 0.001) but not with basal respiration (ρ = −0.075, P = 0.57). Sensitivity analyses accounting for carbonate content and pH showed that aggregate stability, basal respiration, and qCO₂ were comparatively robust, whereas SOC, TN, and MBC responses were partly substrate-dependent. Multivariate analyses revealed coordinated but non-monotonic shifts across the chronosequence. These findings indicate that restoration outcomes in Mediterranean karst cannot be assessed from carbon accumulation alone and that integrating microbial metabolic and structural indicators with edaphic information provides a more informative framework for monitoring afforestation success.