The wooden church was built after 1273. In 1460, Father Paweł of Zator erected the presbytery and began building the sacristy. Further work on the church in the Vistula Gothic style was carried out between 1470 and 1476 by the Kraków Canon, Jan Długosz. The nave, porch,  presbytery vault, and bell tower were constructed. The use of scorched bricks laid in black patterns on the walls and stonework detailing was characteristic. 
It is a single-nave church with a rectangular nave covered with a wooden coffered ceiling, with a narrower presbytery ending in a straight wall with a cross-ribbed vault and an adjoining sacristy. The gabled roof is topped with a ridge turret. Buttresses surround the church. In the porch with contemporary polychrome, there is a stone foundation plaque from 1476 with an inscription and a bas-relief of Saint Margaret. 
The interior is decorated with stonework details, pointed-arch east-facing portals and cartouches with coats of arms. Notable features include the Baroque main altar, by Antoni Frąckiewicz, with a Gothic crucifix from 1440, a painting of Our Lady of the Snows from 1626, a Renaissance tombstone of Father Walenty Brzostowski from 1586, and 16th-century.Renaissance epitaphs. Renaissance polychromes from the 17th century were discovered in the nave in 1963. 
The church belfry has a brick base dating back to 1476 and a wooden top with a 19th-century presbytery and cupola. On the gate in the church wall stand the statues of Saints Margaret and Stanislaus the Bishop. 
The church has been looked after by the Kraków chapter for centuries. That is why, in the summer of 1944, Cardinal Adam Sapieha sent young Karol Wojtyła, a seminarian at the clandestine seminary, here for a holiday. In the years that followed, the future Pope spent his holidays here twice, wandered among the fields where Nowa Huta was to be built, walking as far as the Cistercian Monastery in Mogiła, studied theological works and learned about the problems of the small rural parish.
The indulgence feast for Saint Margaret the Virgin and Martyr falls on the Sunday after 13 July.