The church was built in stages during the Middle Ages. Traces of an earlier church, possibly from the 1100s, have been found near the north wall. In the 1300s the building was extended westwards and the south tower added; in the 1400s the old chancel was replaced with a new one featuring tall vaults and Gothic windows, and it was at this time that the crypt was constructed. Along with Lund Cathedral, Västra Ingelstad church and Dalby church, Skanörs kyrka is one of only a handful of churches in Skåne to have a crypt.
Inside, several furnishings reflect centuries of change and later, sometimes heavy-handed, restoration. A 17th-century pulpit was repainted in 1762 and then stripped of paint entirely some 130 years later, a fate shared by the clerk's and priest's pews. A choir stall assembled in the 1580s incorporates older woodwork thought to date from the 1300s. A late-medieval crucifix hangs in the triumphal arch, also repainted in 1762, though it and the altar escaped the more drastic refurbishment carried out on some other fittings during the 1890s. The font's age is debated: some researchers have suggested a 12th-century origin, though it was more likely acquired towards the end of the 1300s.