Staying in a temple is a wonderful way to really experience Japanese culture. A shukubo stay can be arranged in a variety of places but most commonly in one of the many temples atop sacred Mt Koya.
Staying in a temple overnight is much like staying in a ryokan; you’ll sleep on futon in a tatami matted room and will enjoy a delicious multi-course dinner, although at a temple, this will be shojin ryori; Buddhist vegan fare.