The club's third round tie at Northern of Springburn was abandoned with the Shamrock 2–1 down because of crowd violence, which spilled onto the pitch, and saw the referee and some players injured.

[4] The Scottish FA ordered a replay at Ibrox Park,[5] which the Shamrock won 4–3, in a match "singularly free from rough play", thanks to Breslin finishing off after a "splendid run" from Naughton with just 30 seconds to go.

Later in the season the club beat Royal Albert by two goals to secure the Airdrie Charity Cup for the only time.

[10] The rise of Celtic, which was a greater attraction for fans and players (the Shamrock's Eddie Pearson played in Celtic's first-ever match[11]), and the creation of league competitions, were disastrous for Shamrock, which never secured a place in a league, and was reduced to playing only in cup competitions.

[12] Another blow was losing the right to play at Byresknowes Park at the end of the 1890–91 season, which seems to have caused a split in the club; not only did this result in the formation of a new club, Carfin Hibernians, wearing the same green and white (albeit with hoops rather than stripes), and who managed to secure Byres Knowe Park for the season,[13] ), but two Carfin Shamrocks.

Shamrock's very last match was a 7–3 defeat at Airdrieonians in the final of the Airdrie Charity Cup, at the end of the 1894–95 season, not helped by having to use substitutes in place of three players who had not turned up.

In the 1889–90 Lanarkshire Cup, the Shamrock beat Wishaw Thistle 9–1 in a replay, but an appeal (seemingly because of a delay to the kick-off for want of a ball[27]) saw another replay, which also ended in a draw; with the competition stalled, Wishaw proposed re-drawing the second round in toto, and, when that was voted down, withdrew.

For the final of the Trophy against Motherwell, Carfin borrowed four reserves from Celtic, who had only played second XI football during the season, so were not barred by the rules of the Lanarkshire Cup.

[31] As a consequence of the rule change, the Shamrock refused to defend its trophy[32] after losing 7–1 to Airdrieonians in the main competition's semi-final.

[33] The club's new ground in 1892 caused problems because of the pitch markings; both Airdriehill and Motherwell protested Cup defeats, the former on the basis that the touchlines were not in place (and also that local fans threw stones at the players as they left the village),[34] the latter on the basis that the centre circle and the six yard penalty curves around the posts were missing, but there were lines across the pitch at the 6, 12, and 18 yard lines.