Constructed wetlands built for water treatment often need biomass harvesting to remove nutrients from the system. Usually harvesting is done during the peak growing season to maximize the amount of nutrients removed from the system. This, however, can create huge methane fluxes that escape from plant tissues to the atmosphere. We used manual chambers and eddy covariance measurements to analyze the increase in methane emissions due to the harvesting of two common wetland species, Typha spp. and Schoenoplectus spp., in two climatically different constructed wetlands in Estonia and California. In addition, we determined the biomass nutrient and carbon concentrations from harvested biomass. We found that harvesting during the summer season, e.g. June and August, resulted in a significant release of methane at both sites. At the California site, baseline median methane emissions were 217.6 nmol m−2 s−1, and harvesting resulted in increases to 395.4 nmol m−2 s−1 that decreased to baseline emission within three days. Footprint modeling demonstrated that the emission increases measured by eddy covariance were dominated by contributions from the cut area to the total footprint signal. At the Estonian site, harvesting resulted in methane increases of 15.9 nmol m−2 s−1 to 110.4 nmol m−2 s−1 in August. However, in September and October the emission was significantly lower. Plant biomass analyses showed clear temporal dynamics in terms of nutrient concentration, being highest in summer and lowest in winter. Our experiments indicate that the optimal time for aboveground biomass harvesting is at the end of the growing season before nutrient translocation to belowground plant structures begins coinciding with lowest methane emissions. Therefore, strategic planning of the harvest timing may help reduce greenhouse gas emissions from managed wetlands and thus improve their multi-faceted ecological benefit.