It varies according to the hotel. Below is the list of possible places to store luggage.

Possible to store Luggage	HOTEL GRAN Ms KYOTO HOTEL M’s PLUS SHIJO-OMIYA HOTEL M’s EST SHIJO-KARASUMA HOTEL The M’s KYOTO HOTEL M’s EST NANAJO HOTEL Pagong with M’s M’s HOTEL SANJO OMIYA
Luggage is not possible to store	M’s HOTEL NIJOJO OIKE M’s HOTEL NIJO HOTEL M’s EST SANO WAKOKU HOTEL M’s EST GOJO ODAWARA M’s HOTEL GOJO NAGINATAGIRI M’s HOTEL KYOTO STATION KASUGA HOTEL M’s EST KYOTO STATION TARUYA HOTEL M’S EST KYOTO STATION KIZUYA