The next significant season was in 1901, but that seasson started with another controversy. This time the QRFU had to deal with Ottawa College and Britannia. Britannia protested the match due to what they believed that one of Ottawa's wing man was a non-resident, and the QRFU believed that as well. So on October 16, the match was awarded to Britannia. These two teams met again to determine the QRFU champion, and this time Ottawa College defeated Britannia to capture their fourth championship in the QRFU. In the Dominion Cup match against The Toronto Argonauts the match was called off due to darkness, so the CRU wanted a replay of the match. The replay took place on November 30, in Montreal and this time Ottawa College defeated The Toronto Argonauts 18-3.
The next significant season was during the 1903 season when the Burnside Rules came into effect. Before the seaon started, the Rough Riders decided to return to the QRFU, citing that the competition from the ORFU was not good enough for them but they would not play under The Burnside Rules. Also, Ottawa heard that Brockville did not have enough players to form a club, so they have to resign from the union. At the end of the season, the Rough Riders won the QRFU championship. As for the Dominion Cup, there was none this year due to the fact the ORFU champion Hamilton Tigers were using the Burnside Rules, and that Ottawa refused to play with those types of rules.
The Westmount Football Club replacing Britannia in the QRFU in 1904, the season was underway. By the end of the season, Ottawa College was on top to win the QRFU championship. Like last year, there was no Dominion Title Match because Ottawa College and Hamilton wanted the match to play under each own rules, but neither side budge.
In 1905, Ottawa College left the QRFU so they can join the Inter-Collegiate Union. Ottawa College felt that they have proved that their college style of play was better. In Ottawa College's place, The St. Patrick Pats decided to take their spot. With the Pats now in the QRFU, another development towards the style of the game took place between Montreal and Westmount. This was the first time in history that a game was going to be played in quarters. At the end of the season, The Ottawa Rough Riders won the QRFU championship, and there is going to be a Dominion Cup game, but the question remain who was it going to be against. Ottawa was supposed to play against The Hamilton Tigers, but Hamilton did not want to travel and only wanted to play the match in Hamilton. So, the CRU banned Hamilton, and promoted U of T to play. The style of play that was used in the match was that Ottawa was going to be playing under Quebec Rules (no wing players, and 14 players on the field) in the first half, and in the second half Inter-Collegiate rules (14 players on the field) was enforced. With each team playing under their rules, U of T came out on top, to capture The Dominion Title.
In the 1906 season, Montreal finished the season perfect and captured the QRFU title, but lost to The Hamilton Tigers in the Dominion Title match.
In 1907, Westmount left to join the ORFU, Ottawa and St. Patrick merged to become one club to join Montreal, Toronto, and Hamilton in the new Inter-Provincial Rugby Football Union (IRFU), thus ending the QRFU.