Introducing perennials to traditional cropland is an effective way to increase soil organic carbon (SOC) stocks, but the influence on soil inorganic carbon (SIC) stocks has yet to be understood. Alfalfa-grass-cropland (AGC) rotation involves the initial planting of alfalfa, which gradually degrades into a natural grassland over time, and is eventually reclaimed and converted back into cropland. The effects of AGC rotations with short, medium, and long periods of perennial growth (16, 22, and 27 years from alfalfa planting to natural grassland) on soil total C (SOC + SIC) stocks up to a depth of 2 m were investigated. The AGC rotation had opposite effects on organic and inorganic C stocks. SOC stocks increased with the duration of perennials due to raised soil nitrogen (N) stocks. SOC accumulation, however, was offset by decreasing the SIC stock with a prolonged duration of perennials attributed to soil acidification. Consequently, the soil total C stock increased by only 3 % during 22-year perennial growth, while minimal changes were observed for periods of 16 and 27 years. This study underscores the necessity for increased efforts for SIC management. © 2025 Elsevier B.V., All rights reserved.