The Naruse clan that restored Hojoji traces its line to Naruse Masanari (1567-1625), a trusted fudai retainer of Tokugawa Ieyasu. After serving Ieyasu from his youth and distinguishing himself at Sekigahara and elsewhere, Masanari was assigned in 1607 as chief retainer to the young Tokugawa Yoshinao when Yoshinao was invested as lord of Owari, receiving Inuyama Castle and 35,000 koku — laying the foundations of the Owari Tokugawa house. The Kurihara-branch Naruse, who revived Hojoji, brought Ieyasu's fudai vassalage culture to the Shimousa plain. The temple's status as the only daimyo burial ground in Funabashi attests to how far Ieyasu's consolidation of power reached, even into rural Settsu and Shimousa.

In 1648, the third shogun Tokugawa Iemitsu issued a shuinjo granting Hojoji 30 koku of temple lands. The shuin-ji system was a mark of shogunal recognition extended to leading temples across Japan, and its extension to a provincial temple in Funabashi reflects the deep ties between this area and the powerful local houses of Kasai and Naruse. Renewed by successive shoguns until the fall of the bakufu in 1868, the shuinjo kept Hojoji a privileged temple throughout the Edo period.