The protein sources in feed have a huge impact on good-quality and -quantity meat traits. Yellow lupin (YL) seeds have a similar level of protein as soybean meal (SBM). The most popular is SBM that is genetically modified (GMO). During this age, the consumer market requires non-GMO products. Yellow lupin used as a high-protein substitute for SBM in feed has an effect on the quality of meat from broiler ducks. The aim of the study was to analyse and compare meat quality traits in breast and leg muscles as well as fatty acid (FA) composition in breast muscles from ducks fed mixtures containing YL as an alternative to SBM. Two hundred 1-day-old Cherry Valley ducks were kept in pens on litter in two equal dietary groups, four replications with 25 birds per group. The control group (1) received balanced feed containing SBM. The treatment group (2) received balanced feed containing YL. The feed provided to both groups contained 55% of concentrate and 45% of wheat. Birds received feed and water ad libitum and were reared for 8 weeks. After that, 16 ducks (eight from each group) of BW close to the mean for the whole group were slaughtered. Plucked and gutted carcasses were analysed in a laboratory for quality parameters. Meat was analysed for pH, colour, water-holding capacity and drip loss. Samples of breast muscles were analysed for the content of cholesterol, collagen, intramuscular fat and FA composition. The proposed feed mixture containing YL had no impact on meat traits, content of muscles or fat in duck carcasses (P > 0.05). The values of lightness (L*) and yellowness (b*) and collagen content in breast muscles were significantly higher (P < 0.05) in group 2 (YL). A lower ability to retain water, that is, higher water-holding capacity (percentage of water lost from meat) (P < 0.05), was found for leg muscles from group 2 (YL). The content of C16:0, C18:0, C20:4 n-6, C22:4 n-6, C22:5 n-3, total content of saturated fatty acids (SFA), values of atherogenic index and thrombogenic index were significantly lower (P < 0.05) in group 2 (YL) than in group 1 (SBM). The content of C18:2 n-6 and the polyunsaturated fatty acids-to-SFA ratio (P/S) were significantly higher (P < 0.05) in ducks fed the diet with the inclusion of YL. Diets with YL could be proposed as a partial substitute for SBM in duck-rearing.