Land use changes into and out of agricultural production may substantially influence ecosystem carbon (C) balance for many years. We examined ecosystem C balances for eight years after the conversion of 22 year-old Conservation Reserve Program (CRP) grasslands and formerly tilled agricultural fields (AGR) to annual (continuous no-till corn) and perennial (switchgrass and restored prairie) cropland. An unconverted CRP field (CRP-Ref) was maintained as a historical reference. Ecosystem C balance was assessed using adjusted net ecosystem carbon exchange (NEEadj) calculated by adding C removed in harvested biomass to NEE measured using eddy covariance method. The cumulative NEEadj of the corn and perennial systems on former CRP fields showed that these systems were a net C source to the atmosphere over the 8-year period while on former AGR fields, the perennial systems were net C sinks and the corn system near-neutral. The CRP-Ref was near neutral until a drought year when it became a net source. The corn system on the CRP field will likely reach a new lower soil C equilibrium at least 14 years after conversion but will never regain the C lost upon conversion under current no-till management with residue partially removed. On the other hand, the perennial systems could fully regain in ∼14 years the C lost following conversion. The cumulative NEEadj of the corn systems exhibited a higher C emission than did the perennial systems within the same land use histories, reflecting the dominant role of crop type and management in agricultural ecosystem C balance. Results suggest that converting croplands to grasslands results in immediate C gains whereas converting grasslands to croplands results in permanent (no-till corn with partial residue removal) or temporary (perennial herbaceous crops) net C loss to the atmosphere. This has a significant implications for global climate change mitigation where biomass production from annual and perennial crops is promoted to avoid fossil-fuel C emissions (biofuel) or to remove CO2 from the atmosphere (bioenergy C capture and storage).