Conservation agriculture through no-till based on cropping systems with high biomass-C input, is a strategy to restoring the carbon (C) lost from natural capital by conversion to agricultural land. We hypothesize that cropping systems based on quantity, diversity and frequency of biomass-C input above soil C dynamic equilibrium level can recover the natural capital. The objectives of this study were to: i) assess the C-budget of land use change for two contrasting climatic environments, ii) estimate the C turnover time of the natural capital through no-till cropping systems, and iii) determine the C pathway since soil under native vegetation to no-till cropping systems. In a subtropical and tropical environment, three types of land use were used: a) undisturbed soil under native vegetation as the reference of pristine level; b) degraded soil through continuous tillage; and c) soil under continuous no-till cropping system with high biomass-C input. At the subtropical environment, the soil under continuous tillage caused loss of 25.4 Mg C ha−1 in the 0–40 cm layer over 29 years. Of this, 17 Mg C ha−1 was transferred into the 40–100 cm layers, resulting in the net negative C balance for 0–100 cm layer of 8.4 Mg C ha−1 with an environmental cost of USD 1968 ha−1. The 0.59 Mg C ha−1 yr−1 sequestration rate by no-till cropping system promote the C turnover time (soil and vegetation) of 77 years. For tropical environment, the soil C losses reached 27.0 Mg C ha−1 in the 0–100 cm layer over 8 years, with the environmental cost of USD 6155 ha−1, and the natural capital turnover time through C sequestration rate of 2.15 Mg C ha−1 yr−1 was 49 years. The results indicated that the particulate organic C and mineral associate organic C fractions are the indicators of losses and restoration of C and leading C pathway to recover natural capital through no-till cropping systems.