High above all other buildings in town rose the spires of Bykyrkan(by = village or town). It is sometimes called Storkyrkan (stor = big), because it was one of the largest churches in Sweden. It was dedicated to St. Nicholas, the saint of the seafarers and the merchants. The church was built around the year 1200 and was originally quite a small building. A hundred years later it was extended and by the end of the 14th century a number of chapels were added to the long side of the church. There were six chapels with alters at one side of the church, and seven at the other. At the beginning of the 15th century the church was completed – it was huge, with five naves.
In 1430, King Erik of Pommern declared it "half a cathedral", that is, it was almost on the scale of a cathedral. The church measured 75 by 38 metres. It was built of limestone, with a foundation of grey-stone. The floor was paved with bricks.
A number of priests belonged to the church. They often had German names. The citizens of German origin were probably very influential when members of the clergy were chosen.
If the town was visited by royalty, a celebratory sermon would always be held. One of these grand occasions took place when Erik of Pommern arrived on Trinity Sunday, the 17th of June in 1397. On this day, he was crowned King of the three Scandinavian countries and 133 members of the aristocracy were knighted at the same time.
One of the most well-known priests was Claus (Nicolaus) König, originally a Kalmar boy, who later became Bishop of Linköping, Bishop Nils. Nils continued to live in Kalmar after his ordination.
There was a smaller church in town, Birgittakyrkan, which is mentioned for the first time in the 1440´s. It may have been situated in a building which originally belonged to the Birgitta-sisters of the convent in Vadstena.