[3] By the end of the Thistle's first season, it felt strong enough to challenge the senior Swifts, but the latter club - despite "very poor" play - was still able to win 5–0.

[7] The Scottish Junior FA decided that there had been encroachment by the crowd - around half of whom entered free of charge owing to a failure in organization - and ordered a replay, thanks to the casting vote of the FA President Mr Crawford, who decided he would be referee for the replay.

It entered the Scottish Cup for the first time but lost in the first round 4–2 at home to Cambuslang,[12] who had been runners-up the previous season.

The club also entered the Lanarkshire Cup for the first time, losing to Carfin Shamrock in the second round.

In the former year the club beat Hamilton Academical 5–0 in the first round and drew a bye in the second, before hosting Linthouse in the third in front of a crowd of 2,000.

[15] The club's run in the Lanarkshire Cup in 1889–90 ended in bizarre fashion; after three draws with Carfin Shamrock, and the competition bogged down with outstanding ties, Wishaw proposed re-drawing the second round in toto, and, when that was voted down, withdrew.

Thistle had lost to Airdrieonians in the final the previous season, but, after a dispute with the FA, the Airdrie side withdrew from the competition for 1892–93.

The final, at Dalziel Park in Motherwell, was watched by a crowd of 4,000, and Thistle's goals included two "rushes" where the combined strength of the Jags' forwards carried the ball, and the goalkeeper, over the line.

[19] With the Federation dissolving in 1893, Thistle sought to join the Scottish League, but could not find a seconder to support its application.

The Alliance was reduced the following season to a rump of clubs by another mass exodus, including Thistle, to the new Scottish Football Combination for 1896–97.

[31] Meetings took place in April 1900 with a view to merging the two sides,[32] and on the 30th the members resolved to form a new club, Wishaw United F.C., adopting the Queen's Park colours of black and white hoops, but with both clubs finishing their respective seasons and clearing their debts to avoid any liabilities transferring over.

in the Combination in March 1900 was the club's last on its old pitch, as demolition work started in order to build a new road through the middle.