Cover crops have potential to increase net ecosystem C balance (NECB) and subsequent accrual of soil organic C (SOC) by lengthening the growing season in annual agriculture. By measuring net primary productivity (NPP) and C lost to harvest and heterotrophic respiration (R h ), our objective was to evaluate NECB of annual (winter rye, Secale cereale L.) and perennial (Kentucky bluegrass, Poa pratensis L.) cover crops compared to no cover crop control in continuous maize (Zea mays L.) harvested for either grain or silage. There was no effect of cover crop on NECB, but grain maize NECB was greater than silage (32 vs. −433 g C m –2 ), indicating greater SOC sink when maize residue was retained. Rye was more productive in silage (147 g C m –2 ) compared to grain (32 g C m –2 ). Rye increased total belowground NPP in silage maize (rye: 326, no cover: 275, bluegrass: 268 g C m –2 ) but bluegrass decreased aboveground NPP in grain (rye: 1079, no cover: 1179, bluegrass: 1026 g C m –2 ) and silage (rye: 1037, no cover: 1025, bluegrass: 864 g C m –2 ). Yield was lower under bluegrass (781 g C m –2 ) than no cover (962 g C m –2 ) in silage. Losses of C to R h varied by year, but not by harvest or cover crop. While cover crops may provide multiple benefits to farmers and society, their capacity to directly increase SOC may be low.