Due to the planned limitations in the use of genetically modified soybean meal, the search for alternative sources of protein in animal nutrition is ongoing, which also supports the consumers’ expectations of good quality products, such as eggs. The aim of the study was to assess and compare morphological traits of eggs, fatty acid composition in yolk lipids, and the content and activity of lysozyme in thick and thin albumen in eggs from hens fed a diet based on legume seeds as a substitute for soybean meal depending on the hens age. Analyses were carried out for 300 eggs on dates I–V (19–39 weeks age of hens), obtained from Rosa 1 hens managed in the semi-intensive system. Quality analysis was performed for 30 eggs from each group at a time. The control group of hens (A) was fed a diet based on soybean meal (SBM) and the treatment group (B) was fed a diet based on seeds from narrow-leaved lupin (Boruta), yellow lupin (Mister), and pea (Muza). Eggs were analysed for morphological traits (egg weight, the weight and density of egg components, egg shape index and egg surface area), parameters of albumen (height, Haugh units), yolk colour (La Roche, colorimetry in the CIE Lab system), lysozyme content and activity in albumen, and fatty acids composition in yolk lipids. In group B the egg shape index was higher (p = 0.002), and the eggshell colour index was lower (p = 0.007), as well as the height of thick albumen, Haugh score, and yolk colour (La Roche) were higher in group B (p < 0.05), while redness of yolk was significantly lower (p < 0.001) than in group A. Lower content of C15:0 and C18:1n9 and higher content of C18:2n6 and C18:3n3, (p < 0.05), as well as lower content of MUFA and OMEGA 9, but higher content of PUFA, OMEGA 3, OMEGA 6, PUFA/SFA, OMEGA 9/6 and OMEGA 9/3 were found in group B compared to group A (p < 0.05). There were significant differences in traits between age of hens (p < 0.05). Egg weight, yolk weight and its proportion in egg, as well as shell weight, its strength and thickness increased with the age of hens (p < 0.05). The content of lysozyme and its activity were also higher in eggs from older hens (p < 0.05). Fatty acids composition was beneficial at the beginning and end of the analysed egg production period. The proposed feed mixture based on legume seeds had no negative effect on the quality of eggs, and had a positive effect on yolk colour, the quality of albumen. There was no detrimental effect of diet and age of hens on fatty acid composition of eggs from both groups throughout the study period. To sum up, diet with legume seeds could be accepted as a substitute for soybean meal, due to the beneficial effects for some mentioned traits of eggs. Use of legumes could give a partial self-sufficient for producers from small farms, where is not possible to produce soybean meal. At the same time, the level of anti-nutrients in legumes should be considered.