Although the blue dye indigo has been chemically synthesized for over a century, there is an increasing interest in the indigo plant (Polygonum tinctorium) as a source of natural dyes and medicines. To maintain a stable supply of P. tinctorium throughout the year, we examined the effect of two harvesting methods on the leaf yield of this plant under a closed-cultivation system. With method 8c-M, all shoot branches >8 cm of the stem bottom were harvested and under method 2b-M, all branches, but two, were harvested at the stem bottom. Both methods enabled sustainable leaf yields from the same plants over 1 year. The total weight of shoot branches harvested by 8c-M was 1.86–3.11 times higher that of shoot branches harvested by 2b-M. Harvesting by 8c-M resulted in shoot branch weights lower than those from plants harvested with the 2b-M. Leaf/shoot ratio was increased in plants harvested by 8c-M. The content of indican, the precursor of indigo, in leaves was not significantly different between the two harvesting methods. Our data may provide a new continuous cultivation method of leaf crops all over years in controlled-cultivation systems.