This study used two field trials with 5 and 34 years of liming histories, respectively, and aimed to elucidate the long-term effect of liming on soil organic C (SOC) in acid soils. It was hypothesized that long-term liming would increase SOC concentration, macro-aggregate stability and SOC concentration within aggregates. Surface soils (0–10 cm) were sampled and separated into four aggregate-size classes: large macro-aggregates (>2 mm), small macro-aggregates (0.25–2 mm), micro-aggregates (0.053–0.25 mm) and silt and clay fraction (<0.053 mm) by wet sieving, and the SOC concentration of each aggregate-size was quantified. Liming decreased SOC in the bulk soil and in aggregates as well as macro-aggregate stability in the low-input and cultivated 34-year-old trial. In contrast, liming did not significantly change the concentration of SOC in the bulk soil or in aggregates but improved macro-aggregate stability in the 5-year-old trial under undisturbed unimproved pastures. Furthermore, the single application of lime to the surface soil increased pH in both topsoil (0–10 cm) and subsurface soil (10–20 cm) and increased K2SO4-extractable C, microbial biomass C (Cmic) and basal respiration (CO2) in both soil layers of both lime trials. Liming increased the percentage of SOC present as microbial biomass C (Cmic/Corg) and decreased the respiration rate per unit biomass (qCO2). The study concludes that despite long-term liming decreased total SOC in the low-input systems, it increased labile C pools and the percentage of SOC present as microbial biomass C.