[4] Later the team name was changed to WKS 42 PP, an abbreviation for Wojskowy Klub Sportowy, which means Army Sport Club.

Unfortunately, in June the following year, with the new government in place there was no room for Jagiellonia, mostly because of the history with the Bolsheviks in 1920 and the 42nd Infantry Regiment.

In 1929, it was decided to change districts where Jagiellonia played to the newly formed Białystok OZPN.

At the end of the play-offs Jagiellonia and another team, WKS 82 pp Brześć, were tied for points and had to play one more game at a neutral ground to see who was the winner to that season.

[10] Jagiellonia did win the district championship that season but it was the last trophy they won before World War II.

Most of the players joined Strzelec Białystok and played there for two seasons before World War II broke out in 1939 and closed the first chapter in the history of the club.

Many young players started playing for the club, including future representatives for the Polish national team juniors.

Grzegorz Bielatowicz joined the club as a scout and found a few young talents from the north-east region,[18] among them was Jerzy Zawiślan who was the 2nd top scorer in the II League 1975–76 season who scored 13 goals.

The team was eventually promoted to League II in 1975, but the success was short-lived after only being there for 3 seasons, Jagiellonia was relegated in 1978.

At the end of the 70s Jerzy Bołtuć, Leszek Frelek, Ryszard Karalus and Zbigniew Skoczylas began a large youth project to bring in a strong and young new team.

With Olympic silver medalist Janusz Wójcik as coach, the team played a number of good seasons in Division II finishing third in 1986 and the following year was promoted to I Liga for the first time in the club's history.

[20][21] In addition, the top scorer in the competition was a later representative of Poland, Jacek Bayer who netted 20 times for Jagiellonia.

[26] The first success of the club was the 2009–10 season where Jagiellonia won the Polish Cup, beating Pogoń Szczecin thanks to a goal from Andrius Skerla.

[29] With Mamrots' guidance the club won the silver medal as runners up in a very tight race for the Polish championship, thus earning them a spot in the Europa League for the 2nd time in a row.

[33] On 25 May 2024, Jagiellonia won the Ekstraklasa title for the first time in the club's 104-year history, following a 3–0 win over Warta Poznań on the final day of the season.

[34] In the 2024–25 European campaign, Jagiellonia Białystok started in the UEFA Champions League second qualifying round, defeating Panevėžys with an aggregate score of 7–1 (3–1 at home, 4–0 away).

This led Jagiellonia to the UEFA Europa League play-off round, where they played against Ajax but were defeated 1–7 on aggregate (1–4 at home, 0–3 away).

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

[56] The Polish version reads:[57] W mieście Białystok, W tym w którym żyję, Oddałem serce drużynie.

(2x): Strzelisz 3 bramy, I znów wygramy, Klubie Ty Nasz ukochany!In English it is loosely translated to: In the city of Białystok, Where I live, I gave my heart to my team.

An important objective of Children of Białystok is to engage in sporting life, social and cultural, by organizing sporting events and entertainment for children, young people in schools, orphanages, educational centers, and helping people who are in need financially.

The questioning of Jagiellonia's involvement in the corruption scandal that went through the Department of Discipline of the Polish Football Association started on 20 June 2008, when the National Prosecutor's office in Wrocław handed over documents related to fixing 6 games in the II Liga during the 2004-05 season.

The Department of Discipline of the PZPN imposed a penalty of relegation by one tier in the following season after the judgement became final of five accounts of sports crime.

[64] On 29 April 2009, the court repealed the punishment of relegation, instead handing the club a ten-point deduction for the following season and imposed a fine of 300 thousand złoty.