The aim of the study was to compare Muscovy ducks and mule ducks for proximate analysis, colour attributes, sensory properties of the meat, and concentration of some minerals in the meat and liver, with consideration of the effect of sex on the analysed traits. The study used 46 Muscovy and 44 mule ducks. At the end of the rearing period, 40 birds (10 males and 10 females of each genotype) were selected for slaughter. Meat and liver samples were collected from the slaughtered birds to determine quality traits. The analysed ducks of different genotypes differed significantly in the water content, sodium content, and redness of breast muscles; in the water, fat, and zinc content of leg muscles; and in the sodium, iron, and copper content of liver. Regardless of genotype, males had a higher sodium content in breast muscles; contained more protein, sodium, phosphorus, and magnesium and less potassium and copper in leg muscles; and had a significantly higher content of sodium, potassium, phosphorus, magnesium, zinc, iron, and copper in liver compared to females. The genotype–sex interaction was significant for the sodium and potassium content of breast muscles, for the water, protein, sodium, potassium, phosphorus, magnesium, and copper content of leg muscles, and for the copper content of liver. Our study provided information about differences in the quality of meat and liver in Muscovy and mule ducks.