The impact of organic and conventional crop management together with two variations of conservation tillage was evaluated on N supply and losses at the end of a 4-year Swiss crop rotation. Soil samples were taken from four cropping systems: conventional intensive tillage (C-IT), conventional no tillage (C-NT), organic intensive tillage (O-IT) and organic reduced tillage (O-RT). Laboratory incubations were used to estimate rates of net mineralization, gross nitrification and potential denitrification, while quantitative PCR was used to determine copy numbers of genes of relevant enzymes in these processes. N supply via mineralization and nitrification was unaffected by cropping system. Significant decrease in bacterial ammonia oxidizer (AOB) abundance at the end of the gross nitrification incubation indicated greater responsiveness of this group for activity, in particular under conventional management. C-NT produced the highest potential denitrification, although only significantly different than C-IT. O-RT was similar to C-IT and C-NT in terms of soil N supply and N gaseous losses, meaning that added benefits through its use does not compromise plant N availability or increase N2O losses compared to conventional practices.