A long-term field experiment was conducted from 1989 to 2008 in Estrées-Mons, northern France. From 2000 to 2008, it compared three cropping systems (CS1, CS2 and CS3) varying in crop rotation or growth cycle duration and two tillage treatments: annual full inversion tillage (FIT) and shallow tillage (ST). Soil organic carbon, total nitrogen, bulk density, microbial biomass carbon and nitrogen mineralization rate were monitored during eight years in three soil layers (0-6, 6-20 and 20-30 cm). Half of the experimental plots were sampled every year according to the last ploughing year in ST, so that each plot was sampled every two years. Soil samples were collected in May or June in 2001-2002 (t = 1.5), 2003-2004 (t = 3.5), 2005-2006 (t = 5.5) and 2007-2008 (t = 7.5 years). This dataset includes data on: 1) soil organic carbon and total nitrogen concentration (average of four measurements per plot and layer); 2) soil bulk density, measured with a membrane densimeter for the first layer and with steel cylinders for the other layers (average of four measurements per plot and layer); 3) microbial biomass carbon concentration (one measurement per plot and layer); 4) mineralized nitrogen measured during soil incubation (168 days at 21 °C and a moisture content of 205 g kg-1); 5) nitrogen mineralization rate calculated from an exponential model fitted against the incubation data.