Aims Pulse labeling of crops using 13 C is often employed to trace photosynthesized carbon (C) within crop-soil systems. However, few studies have compared the C distribution for different labeling periods. The overall aim of this study was to determine the length of the monitoring interval required after 13 C-pulse labeling to quantify photosynthate C allocation into plant, soil and rhizosphere respiration pools for the entire growing season of maize (Zea mays L.). Methods Pot grown maize was pulse-labeled with 13 CO 2 (98 at.%) at the beginning of emergence, elongation, heading and grainfilling growth stages. The routing of 13 C into shoot and root biomass, soil CO 2 flux and soil organic carbon (SOC) pools was monitored for 27-days after 13 C-pulse labeling at the beginning of each growth stage. Results The majority of the 13 C was recovered after 27 d in the maize shoots, i.e., 57 %, 53 %, 70 % and 80 %, at the emergence, elongation, heading, and grainfilling stages, respectively. More 13 C was recovered in the root biomass at elongation (27 %) compared to the least at the grainfilling stage (3 %). The amount recovered in the soil was the smallest pool of 13 C at emergence (2.3 %), elongation (3.8 %), heading and grainfilling (less than 2 %). The amount of 13 C recovered in rhizosphere respiration, i.e. 13 CO 2 , was greatest at emergence (26 %), and similar at the elongation, heading and grainfilling stages (~16 %). Conclusions At least 24 days is required to effectively monitor the recovery of 13 C after pulse labeling with 13 CO 2 for maize in plant and soil pools. The recovery of 13 C differed between growth stages and corresponded to the changing metabolic requirements of the plant, which indicated labeling for the entire growth season would more accurately quantify the C budget in plantsoil system.