Since 2001 the Nafferton Factorial Systems Comparison trial has provided a unique facility to investigate factors limiting yields in organic cropping systems. The trial compares two different crop rotations: one cereal-intensive ‘conventional’ rotation and one more diverse ‘organic’ rotation, as well as organic and conventional crop protection and fertility management practices. Analysis of annual yield data allows us to determine whether yield reductions in organic systems are due to rotational history, weed, insect and disease pressure, nutrient limitations, or a combination of these factors. Experience to date indicates that some crops (particularly potato) have yield limitations when grown with only compost as an N source. Recently the trial has been modified to include applications of slurry as well as compost, to try to address the problem of quantity and timing of N supply to the growing crop under organic fertility management. Results will be presented from the 2013 season for winter wheat, potatoes and cabbages grown using various nutrient sources in the background of an organic and conventional crop rotation.