This study compares a traditional agricultural approach to minimise N pollution of groundwater (incorporation of crop residues) with applications of small amounts of biodiesel co-product (BCP) to arable soils. Loss of N from soil to the aqueous phase was shown to be greatly reduced in the laboratory, mainly by decreasing concentrations of dissolved nitrate-N. Increases in soil microbial biomass occurred within 4 days of BCP application-indicating rapid adaptation of the soil microbial community. Increases in biomass-N suggest that microbes were partly mechanistic in the immobilisation of N in soil. Straw, meadow-grass and BCP were subsequently incorporated into experimental soil mesocosms of depth equal to plough layer (23 cm), and placed in an exposed netted tunnel to simulate field conditions. Leachate was collected after rainfall between the autumn of 2009 and spring of 2010. Treatment with BCP resulted in less total-N transferred from soil to water over the entire period, with 32.1, 18.9, 13.2 and 4.2 mg N kg(-1) soil leached cumulatively from the control, grass, straw and BCP treatments, respectively. More than 99 % of nitrate leaching was prevented using BCP. Accordingly, soils provided with crop residues or BCP showed statistically significant increases in soil N and C compared to the control (no incorporation). Microbial biomass, indicated by soil ATP concentration, was also highest for soils given BCP (p < 0.05). These results indicate that field-scale incorporation of BCP may be an effective method to reduce nitrogen loss from agricultural soils, prevent nitrate pollution of groundwater and augment the soil microbial biomass.