Periodic cropping of otherwise permanent pastures can lead to large losses of carbon (C), especially if cropped for maize silage. The long-term effect on C stocks due to periodic cropping depends on whether the lost C is recovered before any future cropping events. Accordingly, this study tested the hypothesis that C lost during periodic cropping would be recovered following a return to permanent pasture within a rotationally grazed New Zealand dairy system. In New Zealand, maize silage is often used as supplemental feed, and its production can be part of the pasture renewal process whereby paddocks are cropped for a year or two before re-establishment of a permanent pasture. The net ecosystem carbon balance (NECB) was measured by combining eddy covariance measurements of the CO2 exchange (net ecosystem production; NEP) with measurements and estimates of all other flows of C for four years following the re-establishment of permanent pasture in a paddock previously cropped for maize silage. The NECB (negative values indicate C loss from the ecosystem) of the four years was –13, –21, –52 and −242 g C m-2 for an aggregated total of −328 g C m-2 indicating further C had been lost. November to January (late spring-summer) was identified as crucial for determining the annual NEP and NECB. NEP during November-January was dependent on climate and farm management. Monthly air temperature negatively correlated with NEP, while rainfall positively correlated with NEP for intervals equivalent to the time between grazing events. Increasing the interval between grazing events to around 28 days during November-January was beneficial for increasing NEP, but longer intervals had limited additional benefit. Small day-to-day management decisions such as the application of effluent, grazing rather than harvesting, and increasing the interval between grazing events have the potential to make small but additive gains to the NECB and provide opportunities to recapture lost C (or minimise further losses) following periodic maize silage cropping of permanent pastures. Data from four years, however, suggests little recovery of previously lost C and indicates that the current return period for periodic maize silage cropping (10–15 years per maize crop) might be too short to maintain C stocks.