In Europe, the most appropriate strategy to replace soybean meal (SBM) in animal feed has been the development of diets containing locally produced protein sources. One of these sources is lupine (Lupinus spp.). The effect of the total substitution of SBM by white lupine (WL) and yellow lupine (YL) seeds in the diets of growing rabbits and of gender on meat quality and the fatty acids (FA) profile were evaluated. Sixty hybrid weaned rabbits (New Zealand × Californian) (20 rabbits per diet), were fed diets that contained 150 g/kg of SBM (SBMD) and WL (WLD) or YL (YLD) for 35 to 69 days. At the end of this period, 30 rabbits (10 rabbits per diet) were slaughtered to evaluate the carcass and meat characteristics and the FA profile of the longissimus dorsi (LD) muscle. In general, the carcass and meat characteristics (pH and colour) were not affected (p > 0.05) by diet or gender. Further, there was no observed effect (p > 0.05) of gender on meat FA and on the calculated indexes related to human health. However, diet had an effect (p < 0.05) on the FA profile, FA categories, and calculated indexes related to human health. The meat from rabbits fed SBMD presented higher (p < 0.05) saturated FA (SFA; 44 vs. 39 g/100 g average on lupine diets) and lower (p < 0.05) polyunsaturated FA (PUFA; 24 vs. 28 g/100 g average on lupine diets). Our results showed that SBM may be completely replaced by WL or YL, improving the quality of LD muscle FA in terms of nutritional quality for humans.