
Clandestine excavation of the temple for artifacts in the year BE 2478 resulted in The Fine Arts Department declaring Wat Yai Chai Mongkhon as a national historical site, and in 2499, Phra Khru Phawanarangsi (Phra Rong Chaiyan) took charge of the restoration of the pagoda. Monks also began to reside and observe the rains retreat (Phansa).
In 2500, Phra Khru Phawan requested cooperation from the Fine Arts Department to conduct further excavation. Golden Buddha images were found beneath the central base of the pagoda along with evidence that treasure hunters were still actively pilfering sacred artifacts. Eventually, a joint resolution with the Fine Arts Department was made to cease all excavations and fill the holes with concrete reinforced with steel to prevent further clandestine excavations.

During the Ayutthaya period, this temple was built during the early reign of King Ramathibodi I, also known as King U-Thong, the founder of Ayutthaya. Legend has it that in the year 1900 of the Buddhist calendar, King U-Thong graciously ordered the excavation and cremation of the bodies of Lord Kaew and Lord Thai, who died of an incurable disease. He then ordered the establishment of a monastery named Wat Pa Kaew (Pa Kaew Forest Monastery). Subsequently, a group of monks from Sri Lanka, who had completed their studies at Ratanamahathat Monastery in Sri Lanka, came to be greatly revered by the people of Ayutthaya.
This led to an influx of people coming to ordain and study at the monastery, leading King U-Thong to establish a new sect called the Nikaya Sangha and appoint a Sangharaja (ecclesiastical head) for this sect, named Sangharaja Phra Wannarat. He held the position of the Sangha’s right-hand preceptor alongside the Sangharaja Phra Phutthakosajarn, who held the position of the Sangha’s left-hand preceptor. Later, he became the teacher of the monks of Wat Pa Kaew Monastery, and because of this, the monastery came to be known as Wat Chao Phraya Thai Nikaya Pa Kaew.
