Abstract The conversion of native vegetation (NV) into agricultural land by clearing and tillage disrupts the soil structure, and depletes soil organic carbon (SOC) pool. The data on changes in SOC pools are needed to enhance scientific knowledge regarding the effects of land use and no-till (NT) systems on soil fertility, agronomic productivity, and soil C sink capacity. Thus, the objective of this study was to quantify changes in SOC fractions due to conversion of NV to agricultural land, and to assess the rate of recovery of SOC fractions and the resilience index of NT cropping systems under sub-tropical (Ponta Grossa/PR — PG) and tropical (Lucas do Rio Verde/MT — LRV) regions of Brazil. The conversion from CT to NT was 29 and 8 years at the PG and LRV sites, respectively. Five different fractions of SOC pools were extracted by chemical methods (i.e., C in the polysaccharides — CTPS, hot-water extractable C — HWEOC, chemically-stabilized organic C — CSOC), and physical fractionation (i.e., particulate organic C — POC, and mineral-associated organic C — MAOC). Land use change primarily altered the labile (HWEOC, TPS, and POC) and also some of the stable (MAOC) pools at both sites. The CSOC pool was almost constant throughout the soil profile and represented, across land uses, 7.2 g C kg − 1 at the PG and 3.1 g C kg − 1 at the LRV sites. At the PG site, the HWEOC and CTPS concentrations in the 0–5 cm depth decreased by 56% (1.21 g kg − 1 ) and 45% (7.21 g kg − 1 ) in CT soil, respectively. At the LRV site, concentrations of HWEOC and CTPS in the 0–5 cm depth decreased by 50% (0.4 g kg − 1 ) and 42% (4.8 g kg − 1 ), respectively. In contrast, concentrations of HWEOC and CTPS fractions in soil under NT in the 0–20 cm depth were closer than those under NV, and exhibited a distinct gradient from surface to sub-soil layers. The adoption of CT reduced POC by 46% (4.7 Mg ha − 1 ), and MAOC by 21% (15.1 Mg C ha − 1 ) in the 0–20 cm depth at the PG site. Using CT for 23 years at the LRV site, decreased SOC fractions in the 0–20 cm depth at the rate of 0.25 and 0.34 Mg C ha − 1 yr − 1 for POC and MAOC, respectively. In contrast, adoption of intensive NT systems in tropical agro-ecoregions increased POC at the rate of 0.23 to 0.36 Mg C ha − 1 yr − 1 , and MAOC by 0.52 and 0.70 Mg C ha − 1 yr − 1 . An important effect to be emphasized is the possibility of recovering, at least partially, the SOC fractions by adopting high biomass-C inputs under NT management, and despite the fact that the experimental duration at the LRV site was only eight years. With a high and diversified input of biomass-C in intensive NT systems, higher resilience index was observed for CTPS, HWEOC, and MAOC. The variation in SOC among CT and NT systems was mainly attributed to the MAOC fraction, indicating that a significant proportion of that fraction is relatively labile, and that spatial inaccessibility of SOC plays a significant role in the restoration of SOC.