Lentil has been overlooked by organic farmers in Europe mainly because of low and unstable yields, notably due to lodging and bruchid beetles. Our study aimed to evaluate the efficiency of lentil-spring wheat intercrops to lower these reducing factors and increase yield and gross margin. A 2-year field experiment was carried out in southwestern France in 2015 and 2016 under organic farming rules. Four lentil and two wheat cultivars were grown as sole crops and intercrops. The “yield gap” concept was adapted to include grain losses due to mechanical harvest and insufficient quality. Mean total intercrop grain yield before mechanical harvest was higher than mean sole crop (1.91 ± 0.47 vs. 1.57 ± 0.29 t ha−1, respectively), with a lower mean yield of lentil in intercrop than in sole crop (1.06 ± 0.28 vs. 1.61 ± 0.54 t ha−1). This led to a lower mean gross margin of intercrop than that of sole cropped lentil (1772 ± 507 vs. 2371 ± 756 € ha−1), before mechanical harvest. The percentage of bruchid-damaged grain did not differ significantly between intercrop and sole crop (41%). However, lentil lodging was lower in intercrop than in sole crop (15 vs. 40%), which strongly increased lentil mechanical harvest efficiency (75 vs. 50%). This led to a similar mechanically harvested yield of lentil in intercrop and sole crop (0.80 t ha−1). Consequently, mean marketable gross margin of intercrops was higher than that of sole cropped lentil (949 ± 404 vs. 688 ± 393 € ha−1), due to the addition of marketable wheat yield. We thus demonstrated for the first time the interest of extending the yield gap concept to consider all grain losses that influence profitability, including those linked to mechanical harvest efficiency and insufficient grain quality. Furthermore, this is a first demonstration of the higher profitability of organic lentil-wheat intercrops compared to sole crops despite the additional costs associated with grain sorting.