[4] The uragaki or notes to Jōgū Shōtoku Hōō Teisetsu mention the eye-opening ceremony of a sixteen-foot Buddha in the temple's Lecture Hall in 685.

[7] The Nihon Shoki records a visit by Emperor Temmu a few months later to the temple of Jōdo-ji, identified by Aston as Asuka-dera but now thought to refer to Yamada-dera.

[4] Records of the temple in the Heian period are scarce, but it is known that Fujiwara no Michinaga visited Yamada-dera in 1023 and expressed admiration for the according to the Fusō ryakuki (扶桑略記).

[5] However, by the end of the following century the Kondō and pagoda had burned and, according to the Tōnomine ryakki (多武峰略記), the temple had become a branch of Tōnomine-dera (today's Tanzan Jinja).

The Yakushi Nyōrai statue stolen from Yamada-dera was destroyed in a fire in the East Kondō in 1411, and only the head survived, which was placed inside the base of the newly constructed principal image.

Excavations have unearthed roof tiles from the Kamakura to Muromachi periods, indicating that the temple was rebuilt on the site of the lecture hall.

The current temple belongs to the Hossō-shū and its honzon is a statue of Jūichimen-Kannon thought to have been made in the late Muromachi period.

[4] The central pillar of the 3x3 bay pagoda rested on a base stone a metre below the podium on which it stood, as in the later examples at Hōryū-ji and Hōrin-ji.

[4][10][11] Beneath, a 1.7 bay section of the wooden outer wall was uncovered, including base stones with lotus designs; columns, with marked entasis; base and head penetrating tie-beams; middle non-penetrating tie-beams; latticed windows; sections of lath for plastering; and bracket blocks.

[4][13] A bronze Buddha head, tentatively identified as that of Yakushi, is the sole surviving element of the principal triad of the former Kōdō or lecture hall.

[18] A statue depicting the Amida Triad with its base inscription 山田殿像 (Yamada-den-no-zō), originally from Hōryū-ji has been attributed to have connections to Yamada-dera, though its true history remains uncertain.

[19] To avoid anisotropic shrinkage and cell collapse during the drying of the waterlogged wood recovered, the architectural members were treated with polyethylene glycol (PEG), a Synthetic fiber polymer used gradually to replace the water content before permanent hardening.