In the area of the Tysiąclecia housing estate under construction, Mass was celebrated by Father Józef Kurzeja, who commuted from Raciborowice, the vicar of the Raciborowice parish to which the village of Mistrzejowice belonged. In 1970, a green–painted barrack with a field altar bearing the image of Maximilian Maria Kolbe stood in the forest, named Zielona Budka. The authorities at the time did not allow a new parish to be established, but Cardinal Karol Wojtyła and the inhabitants of Nowa Huta supported Father Kurzeja. In 1973, a temporary chapel was built on the estate and Zieloną Budką was erected in the churchyard. The church, built between 1976 and 1983 to a design by Józef Dutkiewicz, was consecrated by Pope John Paul II during his second pilgrimage to his homeland.

The church has two levels, a vicarage, and 10 catechetical rooms. The walls of the church and vicarage were clad in white Pińczów stone, and the staircase was lined with red Szydłowiec sandstone. The upper church seats 5,000 worshippers. The main altar features a statue of Christ Crucified almost six metres high, as well as a statue of Our Lady of the Immaculate Conception and one of Saint Maximilian Maria Kolbe. The tabernacle is supported by angel figures. All sculptures are the work of Kazimierz Gustaw Zemła. The baptismal font, cast in bronze, commemorates the baptism of the Polish-Lithuanian Commonwealth. In 1982, Pope John Paul II donated red Swedish granite to the church for the floor and white Carrara marble for the altar, the background of which was made of Italian travertine.

The lower church holds 2,000 worshippers. In the burial crypt is the marble sarcophagus of Father Józef Kurzeja. Above the altar hangs a statue of Jesus Crucified, the work of sculptor Bronisław Chromy, and on the sides are Orthodox images of saints. Father Henryk Jankowski, Father Jerzy Popiełuszko and Solidarity leader Lech Wałęsa attended mass here.

A monument to John Paul II, designed by Professor Gustaw Zeła, was unveiled on the church square in 1991, and in 2006, a stone obelisk with the image of Father Kazimierz Jancarz was erected nearby. After martial law was declared in Poland on 13 December 1981, Father Kazimierz Jancarz became Chaplain to the Workers. Seeing their growing activity in the parish in Mistrzejowice, he founded the Working People's Chaplaincy. Since 1984, Thursday masses for the Homeland have been held here, gathering thousands of the faithful.