He was ordained a Roman Catholic priest on 24 April 1897, by the Auxiliary Bishop of Mogilev, Franciszek Albin Symon.

At Christmas 1901 he met the foundress Feliksa Kozłowska and was deeply impressed by her spirituality and ambitions for the Polish clergy.

Despite his modest social background, his forceful personality enabled him to overtake the influence of other well educated and high-born clerics in her circle.

That year, the provincials of the Mariavite order presented the texts of Kozłowska's visionary revelations and a history of the movement to the Bishop of Płock, Jerzy Józef Szembek and to the archbishops of Warsaw and of Lublin in the hope of gaining ecclesiastical approval.

In February 1906 the priests' group informed the Holy See that it was separating from the jurisdiction of the Polish bishops, but it asked its cause to be adjudicated by Rome.

In April 1906, Pius X promulgated the encyclical, Tribus circiter which maintained the decision of the Holy Office regarding Kozłowska and the Mariavite community.

[7] In the face of the terminal set-back, Kowalski with Kozłowska set about codifying the movement's doctrines and beliefs.

A glimmer of hope appeared when in a move calculated to snub the Polish Catholic authorities, the Russian government recognized the Mariavite movement as a "tolerated sect" in November 1906.

Then, through the good offices of Russian General Alexander Kireyev, the leadership was permitted to contact the Old Catholic Church of the Netherlands.

As the ailing Kozłowska's influence waned so the forceful Kowalski had free rein to mould the new church to his liking.

They were soon organizing kindergartens, schools, Literacy classes, libraries, kitchens for the poor, shops, printing houses, poorhouses, orphanages factories and animal husbandry.

He had two highly qualified and experienced architect/engineers among the Mariavite priests, Szymanowski and Przysiecki, who delivered the plans and oversaw the construction.

The Mariavites then bought an estate of 5 square kilometres (1.9 sq mi) near Płock which was named Felicjanów after Kozłowska.

The outbreak of World War I, although a terrible ordeal for the millions involved, eventually benefited the country, in that it regained its sovereign independence after 120 years, while the Mariavite Church garnered more adherents.

Kowalski himself appeared in 20 cases: among the charges were: blasphemy against God, the Bible, the Catholic Church, and the sacraments, then betrayal of the country, of socialism, communism, theft, fraud etc.

However, his radical reforms, preaching Donatism and his modernistic approach disrupted the connection with the Old Catholics, who were then firmly opposed to the ordination of women and broke off fellowship in 1924.

During the extended trip he met with representatives of Eastern Orthodox Churches, in Serbia, Bulgaria, Greece, Turkey, Palestine and Egypt.

In October 1934, the other bishops and priests demanded changes in the teachings and rules of administration in the church, but Kowalski refused to agree.

After the outbreak of World War II in September 1939, Kowalski wrote a letter to Adolf Hitler in which he criticised the annexation of the Polish coastline and invited the German chancellor to consider becoming a Mariavite, among other observations.

The effect was to create the invader's interest in a small religious community that could present difficulties in the General Government.

Jan Kowalski was murdered in 1942, at age 70, at the Nazi Hartheim Euthanasia Centre in Alkoven, Ostmark (Austria).

After his death, the Felicjanów Mariavite community recognised Jan Maria Michał Kowalski as a holy martyr.

Mariavite settlers gave his name to a new village, Michałowo, Płońsk County Jan Kowalski was a prolific writer, translator and editor.