This meta study on the crop yield gap suggests that organic farming has about 80% the yield of conventional farming at the field level, yields may vary widely and organic yields can surpass conventional yields. The authors state:
Our analysis of yield gaps was at crop and field level. The results cannot readily be upscaled to higher system levels. Organic agriculture relies for its crop nutrients on natural soil fertility, legume crops, compost and manure. When legumes are grown as a green manure crop instead of a food or fodder crop to add nitrogen to the system, the average yield of food and fodder crops over the entire rotation is reduced. [...] We did not perform an in-depth analysis of this issue for our data, but it may be assumed that at crop rotation or farm level at least some organic yields in our database would have to be reduced to account for non-productive green manure crops.
Another important source of nutrients in organic farming is manure. Some of the successful organic production systems are dependent on relatively large manure applications imported from outside the farming system (e.g. Clark et al., 1999; Jaim and Al Kader, 1998). If these systems were to be adopted more widely in a given region, manure may become a limiting resource, thus reducing overall organic food crop yields (e.g. Jaim and Al Kader, 1998). [...]
In conclusion, a thorough analysis of the productivity of organic and conventional agriculture at crop rotation, farm and regional level is needed that accounts for the availability of crop nutrients. Since maintaining soil fertility is generally a greater challenge for organic systems (e.g. Nguyen and Haynes, 1995), we hypothesize that at higher system levels yield gaps of organic agriculture may be larger than 20%.
So I'm looking for research that compares organic with conventional agriculture at the farm level, as at this level the diminished yields due to green fertilization would be taken into account. Crucially for me to understand are the nutrient/fertilizer flows, so ideally the study would also compare organic yields at different (external) fertilizer inputs. But I'll take what I can get.