Yoshimitsu is enshrined with his grandfather MINAMOTO no Yorinobu, his father MINAMOTO no Yoriyoshi, and his older brothers MINAMOTO no Yoshiie and MINAMOTO no Yoshitsuna at Tsuboi-gongen, which is next to Tsuboi Hachiman-gu shrine, where the ujigami (the guardian deity) of the Kawachi-Genji is enshrined; Tsuboi-gongen is located in Tsuboi in Ishikawa county of Kawachi province (present-day Tsuboi in the city of Habikino in Osaka Pref.), which was the seat of the Kawachi-Genji's power as well as where Yoshimitsu is believed to have been born.
また、生誕地と思われる河内源氏の本拠地の河内国石川郡(大阪府)壷井（現在の大阪府羽曳野市壷井）にある河内源氏の氏神の壷井八幡宮と並ぶ壷井権現に、祖父源頼信、父源頼義、兄源義家、兄源義綱と共に祀られている。