Feeding a low-protein diet supplemented with essential amino acids to laying hens is known to reduce excretion of nitrogen. We reported that the laying hens fed low-protein diets reduced nitrogen excretion and environmental gas emissions during manure composting without affecting egg productivity, recently. However, there are few reports on effects of low-protein diets on egg production, nitrogen excretion and quality of layer manure compost in commercial layer farms. In this study, we fed laying hens 2%-lower crude protein (CP) diets supplemented with additional amino acids (LCP) or farm’s conventional diets (Cont) in a commercial layer farm. We then investigated the egg production performance of the laying hens, the nitrogen excretion and several characteristics of the layer manure compost. The egg production performance of the laying hens was calculated based on the number of eggs and birds every day, and egg quality was measured. The nitrogen excretion was calculated by collected total amount of excreta. Regarding characteristics of the manure compost, the composition of the manure compost and the germination rate and growth of Komatsuna using the manure compost were measured. There were no significant differences in the egg-laying rate and the egg quality between the hens fed LCP and Cont. However, the LCP-fed laying hens had lower dry weight of manure excretion and nitrogen excretion (early laying period, 1.85 g/layer/day vs. 1.54 g/layer/day; later laying period, 1.19 g/layer/day vs. 0.77 g/layer/day) compared with the Cont-fed laying hens. The concentration of total nitrogen, total phosphate and total potassium, carbon-to-nitrogen ratio and germination percentage of Komatsuna of the manure compost of the Cont-fed and the LCP-fed laying hens were similar. Furthermore, the manure compost of the Cont-fed and LCP-fed laying hens showed no difference in the growth test of Komatsuna. These results indicate that, in this study focused on the whole egg production system, feeding 2%-lower CP diets supplemented with additional amino acids to laying hens in the commercial layer farm decreased the nitrogen excretion without affecting egg production performance and manure quality.