The impact of transient carbon depletion on reproductive growth in Arabidopsis was investigated by transferring long-photoperiod-grown plants to continuous darkness and returning them to a light-dark cycle. After 2days of darkness, carbon reserves were depleted in reproductive sinks, and RNA in situ hybridization of marker transcripts showed that carbon starvation responses had been initiated in the meristem, anthers and ovules. Dark treatments of 2 or more days resulted in a bare-segment phenotype on the floral stem, with 23-27 aborted siliques. These resulted from impaired growth of immature siliques and abortion of mature and immature flowers. Depolarization of PIN1 protein and increased DII-VENUS expression pointed to rapid collapse of auxin gradients in the meristem and inhibition of primordia initiation. After transfer back to a light-dark cycle, flowers appeared and formed viable siliques and seeds. A similar phenotype was seen after transfer to sub-compensation point irradiance or CO2. It also appeared in a milder form after a moderate decrease in irradiance and developed spontaneously in short photoperiods. We conclude that Arabidopsis inhibits primordia initiation and aborts flowers and very young siliques in C-limited conditions. This curtails demand, safeguarding meristem function and allowing renewal of reproductive growth when carbon becomes available again. We investigate how reproductive growth responds to a transient shortfall in carbon in the indeterminate weed Arabidopsis. Transfer of long photoperiod-grown plants to continuous darkness or low light or CO2 resulted in massive abortion of flowers and very young siliques but the apex function was maintained, and flowering and seed set resumed when the plants were transferred to a light-dark cycle. The same phenotype appeared spontaneously in short photoperiods, where growth is carbon-limited. This response represents a good strategy to optimize seed formation in a fluctuating environment in indeterminate species but results in a window of vulnerability when flowering is synchronized, as has happened in many crops.