Originally built in the 14th century in Masovian Gothic style, the cathedral served as a coronation and burial site for numerous Dukes of Masovia.

The archcathedral was connected with the Royal Castle (Zamek Królewski w Warszawie) by an elevated 80-meter-long corridor that had been built by Queen Anna Jagiellonka in the late 16th century and extended in the 1620s after Michał Piekarski's failed 1620 attempt to assassinate King of Poland Sigismund III in front of the cathedral.

The profuse Early Baroque decoration inside from the beginning of the 17th century and magnificent painting on the main altar by Palma il Giovane depicting Virgin and Child with St. John the Baptist and St. Stanisław were destroyed in German bombing of the church on August 17, 1944.

The painting of the Virgin and Child was created in 1618 for King Sigismund III Vasa especially to place on the central altar of the St John's Cathedral.

Among the sculptures lost due to German bombardment, the most worthy of mentioning was a marble bust of Jan Franciszek Bieliński, voivode of Malbork (died 1685), carved by Jean-Joseph Vinache.

There is a pulpit from 1959, designed by Józef Trenarowski and stalls which are a replica of the destroyed baroque ones, founded by King John III Sobieski.