The Cathedral of Santa Mara de Sigüenza and the Mudejar church of Santa Mara de la Fuente la Mayor make up the two episcopal sees of the Diocese of Sigüenza-Guadalajara, respectively. Construction began on it about the year 1300. With a central portico sporting a horseshoe arch and two flanking ones sporting tumulus arches, the interior is divided into three naves. Francisco Mir's major altarpiece in the Mannerist Renaissance style really stands out. One bell dates back to the 18th century, while another two date to the 19th, and the remaining five were all cast in the 20th. Among the city's most revered churches, this is a place of spiritual significance.

The exterior of the church is mostly unchanged from when it was first built. The primary access to the building is located on the side that faces the Plaza de Santa Mara. Another door may be found on the south wall, and a third, now-forbidden one can be seen in the wall of the former sacristy, which was connected to this side of the church. The pointed horseshoe arches that comprise these doors are characteristic of the Mudéjar style, which may be found across Syria.

Exposed brick is used throughout, with the arch constructed by brick projections arranged radially and bordered by a course of brick forming simple loops in sections, some of which contain green ceramic bits. They are framed by squat pillars, and the western alfiz is adorned with brick projections organised in a radiating pattern that converges on the door's centre. These projections mirror the design of the entryway itself, serving as an impost made from the same material. A replica of the main door was installed in the former sacristy.

An arcade built in the early 16th century in the Renaissance style of Alcarria supports the walls on the south and west. Masonry forms the outer walls of the church, and brick courses separated by various renderings form the inner walls. The transept's square lantern, constructed at the turn of the 17th century, is made of brick like the rest of the church.

This church's tower is attached to the south wall, close to the chancel. Clues suggest it was formerly cut off from the remainder of the church. It's a square building with thick brick walls that are only broken up in two places by narrow arrow slits that shine light on the intriguing staircase leading up to the bells, which are protected by towering semicircular arches that in turn are framed by lines of brick that are lavishly decorated with games and combinations. Above this 16th-century portion is a more recent one that culminates in a spire in the Madrid style and is topped by a cornice that is also made of brick.

It is divided into three aisles by massive pilasters and semicircular arches, has a transept highlighted by a dome topped with a lantern, and an elevated presbytery. Plaster was used to create the nave ceiling, and above it was found an ancient Mudejar coffered ceiling that had been carefully conserved. A choir loft may be seen at the church's basement level.

Both sides have churches with chapels. The Figueroa and Torres family chapel can be seen in the former sacristy's location in the epistle nave. There are several tombstones and a good marble altar from the 19th century there to honour this noble family's passing. The Visitation Chapel, constructed in 1480 by Don Alonso Yáez de Mendoza, an ancestor of Cardinal Mendoza, is at the front of this nave. The old chapel is long gone, leaving just the alabaster reclining statue of woman in religious garb and praying hands. The neoclassical niche with the hooded Yáez coat of arms was erected by a descendent in the 18th century, while the rest is a later addition.

Both Juan Sánchez Hurtado, a commissioner of the Inquisition and priest of Santa Mara in 1636, and Manuel de Albornoz y Sotomayor, another priest of the church and the benefactor of the high altar's construction in the first quarter of the 17th century, are memorialised by tombstones in the gospel nave, each bearing a coat of arms. On this wall is a painting of the Virgen de la Varga. The Santsimo family chapel, established by the Guzmán family at the turn of the 16th century and where all of its members were buried until the turn of the 19th century. The polychrome Guzmán arms adorn the doorway, while the chapel's interior is adorned with multiple enormous coats of arms depicting the family's different links and with this legend:

The M.N. Cavo don Lus Guzmán and Mara de Guzmán, his wife, SSres. de la Villa de Alvolleque Lugar de Burramiento y descanso and their suzesores in their home and Mayorazgos, founded this chapel in honour of Our Lady of Peace and Mercy so that they, their children, and any other people they deem worthy of honouring in death may be laid to rest here.

The centre nave, beneath the presbytery, is littered with tombstones and tombstone fragments.

Viewers in the presbytery will be treated to a polychrome Plateresque altar frontal and pulpit. Don Juan Morales, a native of Guadalajara, was buried there, and his tomb may be seen on the gospel wall. A late-15th-century statue of the donor kneeling on a cushion and wearing a bonnet while praying can be found beneath a contemporary arcosolium. He sees a beautiful half-relief depicting the Resurrection, complete with four individuals and a landscape, before him. The individual's coat of arms appears above the others.

An impressive altarpiece by an anonymous artist from the first third of the 17th century hangs in the back of the presbytery. It has two sections and three aisles, and the exhibition spaces are filled with magnificent scenes of carving in relief depicting events from the Virgin's life such as the Nativity, the Epiphany, and others, with a magnificent depiction of the Assumption of Mary at its centre and a Calvary atop the building. It is moderately and elegantly executed in its carvings and structural characteristics, and it is polychromed in the style of the Renaissance.