The original location of the shrine was in Nubia, 15 kilometers (9.3 miles) south of Aswan, near the first cataract of the Nile and the religious center in Philae, dedicated to the goddess Isis. In the early 2nd century BC, the Kushite king of Meroë, Adikhalamani (Tabriqo), began construction by building a small chapel for the god Amun. This chapel was decorated in a similar style to the Meroitic chapel, which later became the Temple of Dakka. Later on, during the reigns of Ptolemy VI, Ptolemy VIII, and Ptolemy XII of the Ptolemaic dynasty, the chapel was expanded on all four sides to become a small temple measuring 12 by 15 meters (39 ft × 49 ft), dedicated to Isis of Philae. The Roman emperors Augustus and Tiberius completed the temple's decoration.
To reach the stone enclosure wall of the shrine from the quay, there is a long processional way that passes through three stone pylon gateways and leads to the temple itself. The pronaos, which had four columns with composite capitals, collapsed in 1868 and is now lost. Behind the pronaos lay the original sanctuary of Amun, the offering table room, and a later sanctuary with several side-rooms and stairs leading to the roof.
In 1960, UNESCO called for the preservation of Egypt's historical legacy due to the construction of the Aswan High Dam, which threatened several monuments and archeological sites. As a token of appreciation for Spain's assistance in saving the Abu Simbel temples, Egypt donated the Temple of Debod to Spain in 1968.
The temple was reconstructed in Parque del Oeste, a park in Madrid, and opened to the public in 1972. However, the gateways were rearranged differently than their original placement, as seen in a photo of the original site. The temple is a unique example of ancient Egyptian architecture outside of Egypt and the only one in Spain.
Criticism from Egyptologists about the temple's continued exposure to the elements prompted the Madrilenian city council to unanimously decide to hasten plans to cover the monument in February 2020, unlike other donated temples.