The club was founded in 2008 when a group of university students decided to participate in IV liiga South, which is 6th and also the lowest tier of Estonian football pyramid.

History of the club begins a year before the official founding of Tartu JK Welco Elekter when group of football enthusiasts, led by charismatic first captain of the team and eternal head coach Mirko Kikkamägi, gathered under the name JK Masuudinaine to compete in local Tartu football championship in November 2007.

JK Welco Elekter won its first trophy in annual Estonian Football Association End of Year tournament when the club was 3rd.

Mikk Valtna was named MVP of the tournament In the second season, the team was much more experienced and experimental strategies of young football mastermind, head coach Mirko Kikkamägi, started to succeed.

Addition of experienced centre-back Juri Avdonin and former member of Estonian youth national team, winger Marti Pähn, gave the squad much needed depth, but Welco still struggled to find the back of the net in the 1st round, with star striker Mikk Valtna abroad.

Estonian Cup was a success for the team, since Welco advanced to 1/16-final and just narrowly missed the target, by losing away to Meistriliiga side FC Kuressaare 1–2.

The team saw the departure of beloved lean mean goal machine Mikk Valtna, who joined inner-town rivals Meistriliiga side JK Tammeka Tartu.

All things considered, spring round was unsuccessful for the team and club's chair decided to part ways with head coach Boris Hrabrov.

The return of Rassulov and addition of former Estonian u-14 youth national team player Marten Kihho helped to achieve 5th place in the league at the end of season.

Also, the Estonian Cup was a huge success for the club – team advanced to 1/8-final and missed further stage of the competition by only the narrowest of margins – Esiliiga side FC Puuma defeated Welco in front Tartu home crowd 4–3.

Season 2014 started with high ambitions – new off-season acquisitions Erki Kade, former Estonian U19 national team winger Siim Sillaots and Siim Kaasik from the in-town rivals Tartu SK 10 gave the electricians starting 11 a level of quality that proved to be enough to play for the highest places in the league.

Additionally, strong and experienced centre-back Lehar The Terminator Savikink and nimble target-man Hannes Tiru from FC Levadia joined the ranks and improved the quality of the team.

The first season in the top leagues of Estonian football pyramid was a challenge for the club, since it brought more games, higher playing level and requirements for the organization.

Although Welco lost the first game at home 2:4, the Estonian football community was rocked by the infamous Hendrik Pürg Scandal.

Kikkamägi left the head coaching position to concentrate on his playing career and vacant job went to experienced Boris Hrabrov.

Club decided to change the head coach once again in the middle of 2012 season – due to the underperforming team and lack of enthusiasm on field.

After Mikk's decision to rejoin the black-white army of Welco on the field, Siim Valtna was the lone head coach of the first team.

During the 2010 season, club decided to change its appearance drastically and introduced distinctive black-on-white hoops design for shirt.

The winning jersey was a combination of white base with red back (that symbolizes the flag of club's home town Tartu), and already "legendary" black stripes.

The competition lasted for a week, gathered a whopping 1400 votes and had a total reach of 100,000 people on club's Facebook page.

In the beginning of 2010 season, Welco moved its home ground to Annelinna kunstmurustaadion, mainly due to renovation of Tamme artificial turf.

On 10 June 2023, Tartu Welco opened their very own home ground Holm Jalgpallipark, which the club had constructed for five years.