The ancient temple, long intertwined with the history of Ayutthaya, was originally named Wat Kokkhuai. It was honored as a royal monastery during the Thonburi period in 1782 under the reign of King Buddha Yodfa Chulaloke. The king graciously commissioned the construction of a small ubosot (ordination hall) and granted boundaries to the temple, renaming it Wat Kokkabue. Later, during the reign of King Nangklao, he commissioned Prince Krai Sorawichit to oversee the restoration of the ordination hall at Wat Yan Nawa, previously restored by King Buddha Yodfa Chulaloke. He also ordered the construction of a stupa, uniquely designed with a base resembling a Chinese-style junk boat, the only one of its kind in Thailand, completed in 1844. In addition, two new monk's quarters were built, with gold leaf adorning the gables, doors, windows, and entrance arches of the ubosot at the same time. Apart from the striking junk boat stupa, the ubosot of this temple is regarded as a premier piece of art from the Rattanakosin period, featuring a gable crafted by royal artisans during the reign of King Rama I, decorated with heavenly figures and mythical creatures from the Himmapan forest. Inside the ubosot, there are four principal Buddha statues in the subduing Mara pose, each of varying sizes. Adjacent to it is the Tripitaka Hall, a three-story building designed in traditional Thai style, topped with three spires. This hall houses cabinets for the Tripitaka, important Buddhist scriptures, as well as Dhamma books and a memorial of King Nangklao, located in front of the uniquely designed stupa, inviting both tourists and the general public to pay their respects.