The village was established in 1345 when Warmian bishop Herman of Prague issued its first privilege confirming the foundation.

[2] The village administrator also received a permit to run an inn with a beer tavern and the right to fish in the lake called Rauthschoys and to hunt in the surrounding forests (for his own needs).

In 1356, the bishop of Warmia, Jan Stryprock, enrolled Jonkowo in the collegiate chapter in Dobre Miasto.

In 1454, King Casimir IV Jagiellon incorporated the region to the Kingdom of Poland upon the request of the Prussian Confederation.

During the Swedish invasion of Poland (1701–1706), in 1703, Jonkowo (as well as other nearby villages) was burdened with a high contribution, which led to its ruin.

After the epidemic in Warmia ceased, when the cult of St. Roch, the patron saint against the plague, developed, Jonkowo was visited by numerous Warmian pilgrimages.

On June 14, 1715, the church was consecrated again by the Auxiliary Bishop of Warmia, Jan Franciszek Kurdwanowski [pl], in honor of St. John the Baptist and St.

[3] Bishop Krasicki encouraged the local population to maintain a newly built school, to which the Prussian government donated 100 thalers.