Malting barley (Hordeum vulgare L.) is traditionally grown under low soil fertility as a conservative approach to achieve the malting requirement of grain below a maximum prescribed limit for protein concentration, typically 12.0%. Such strategies severely limit grain yield. Traditionally, barley breeders have sought to improve yield in malting barley through selection for higher yield per se, without considering an alternative approach in which genetic manipulation of inherent grain protein concentration would allow higher yields through the adoption of an alternative farming system for malting barley production. The present study examined whether greater yield improvements could be achieved by manipulating genes influencing grain protein content, and allowing malting barley to be grown on crop rotations with higher fertility. Doubled haploid lines, selected from a mapping population based on allelic differences at two genes (quantitative trait loci; QTL) influencing grain protein content, were evaluated for productivity over a range of agronomic practices and environments (sowing date, nitrogen application, and a range of field histories). QTL effects were highly repeatable over the range of practices and environments, with individuals carrying two low-protein alleles (q(1) q (1)q (2) q(2)) producing grains with comparatively lower grain protein than individuals carrying the alternate allelic configuration (Q(1)Q(1)Q(2)Q(2) ). Based on two years of data, the yield advantage of growing barley on legume stubble as opposed to wheat stubble was approximately 1.0 t ha(-1), or a yield increase of 53.3%. When grown after a pulse crop in 2005, average yields of those mapping population genotypes carrying low-protein alleles was 4.28 t ha(-1), with average grain protein of 12.0% whilst the average yield of their high protein counterparts was 3.76 t ha(-1) with an average protein level of 12.7%. We conclude that, as an alternative means of malting barley yield improvement, varieties can be developed that allow barley to be grown in highly fertile conditions resulting in yields up to 53% over current farming practices, while maintaining protein levels within malting specifications.