Integrated weed management, which allows reducing the reliance of cropping systems on herbicides, is based on the use of specific combinations of innovative agricultural practices. However the impact of the introduction of these practices in cropping systems may influence soil functioning such as biogeochemical cycling. Here, we investigated N2O emissions and the abundances of N-cycling microorganisms in 11-year old cropping systems (i.e. conventional reference and integrated weed management) in order to estimate the environmental side-effects of long-term integrated weed management. N2O emissions were continuously measured using automated chambers coupled with infrared analysers. Abundances of ammonia oxidizers and denitrifiers together with total bacteria and archaea were determined monthly from 0 to 10 and 10–30 cm soil layer samples by quantitative Polymerase Chain Reaction (qPCR). The relationship between N2O emissions and microbial abundances during the study were investigated as were their relationships with soil physicochemical parameters and climatic conditions. Over 7 months, the system with integrated weed management emitted significantly more N2O with cumulated measured emissions of 240 and 544 g N-N2O ha−1 for conventional and integrated systems, respectively. Abundances of microbial guilds varied slightly between systems, although ammonia-oxidizing bacteria were more abundant in the reference system (1.7 106 gene copies g−1 dry weight soil) compared to the integrated system (1.0 106 gene copies g−1 dry weight soil). These differences revealed both the long-term modification of soil biogeochemical background and the functioning of microbial processes due to 11 years of alternative field management, and the short-term impacts of the agricultural practices introduced as part of weed management during the cropping year. The abundances of the different microbial communities involved in N cycling and the intensity of N2O emissions were not related, punctual high N2O emissions being more dependent on favourable soil conditions for nitrifying and denitrifying activities. Future studies will be performed to check these findings for other pedoclimatic conditions and to examine the impact of such cropping systems.