Archaeological research done in the past few years has proven that in the location of today’s church there was originally a complex of wooden houses on posts dating back to the 12th century. At the start of the 13th century, a temple was built in this very location. Its foundations were uncovered beneath the presbytery of today’s church and beneath the Mikuláš (Nickolas) Chapel. It had a rectangular shape which was finished with an apse. The construction of the Church of Saint John the Baptist was begun after about 1250. Ranking this building as the oldest architectural monument in the city, it was this construction phase where the following were done: the completion of the southern side aisle, which has been preserved to this day, and the establishment of the position of the nave and semi-circular arcades between them, which made use of products from the Cistercian ironworks in the style of what is known as písecko-zvíkovské gotiky (Písek-Zvíkov gothic).
The church was originally intended to be a triple-nave basilica; however, the northern aisle was never built. Before 1320 the temple was acquired by the Minorite order, which completed the building in the mid 14th century. The most valuable part of the ornate painted interiors was done during this period. The area of the nave was closed in with a flat beam ceiling; the late gothic star vaulting was not done until the end of the 15th century. Building activities in the complex continued. The Saint Nicholas Chapel was built in the 1360s at the south side of the presbytery, with a jumping vault towards the central column and opening towards its own small presbytery on the eastern side. This chapel is considered as the direct predecessor of South Bohemian double-nave churches, therefore an important work of exemplary gothic style.
At the beginning of the 17th century, the presbytery of the church was furnished with new late renaissance pews; a century later new baroque pews were also installed in the main nave. In the second half of the 17th century, the main altar was fit into the church, and at the beginning of the 1700s a pulpit with an older statue of Saint John the Baptist was installed. After the dissolution of the Jesuit order, the side altars from the Chapel of Saint Mary Magdalene were brought here (devoted to Saint Francis of Xavier and Saint Ignatius of Loyola) and exhibited in an exhibition of religious art. In the interior there are numerous tombstones, the most precious of which are the gothic tombstone of Magdalena of Gleichen, dating back to 1492, and the renaissance tombstone of Lord Španovský of Lisov.
The building of the Minorite monastery is adjacent to the northern side of the Church of Saint John the Baptist. The central ”paradise” courtyard is encircled by the cloisters, with their ribbed vaulting of late gothic origin. Previously, the arcaded passage appeared to be less imposing, as it had a simpler flat beam ceiling, similar to the main nave. In 1369 the agreement for the reconstruction of the arcaded passage was made with the builders of the monastery in Třebon, master builders Mikuláš and Ondřej (Nicholas and Andrew), who constructed its architectonically most valuable west side. This is the side from which one enters the Soukenická (Drapery) Chapel, originally the monastery capitural hall with vaulting to the central column. From the 1450s there were other reconstructions made, which included the elaborate ornamentation of the monastery’s arcaded passage. The oldest frescos originated before the late gothic reconstructions, which partially damaged them. Some better preserved and more extensive paintings from later periods are dispersed around the whole perimeter of the arcaded passage.
After the departure of the Minorites in the mid 16th century, Jáchym of Hradec had a hospital added to the west side of the monastery, which included two magnificent renaissance halls on the ground floor. There were no other significant changes to the monastery after that, except the addition of a baroque chapel in the corner between the northern and eastern wing of the arcaded passage. The complex had several fires and the buildings gradually deteriorated, although they mainly served as a hospital, and later as a hostel for tourists. At the end of the 20th century and the start of the 21st, the whole complex underwent expensive reconstruction and is now used by the Jindřichův Hradec Museum.