Upon rejoining Arsenal, Scott helped the club to a domestic double of the FA Women's Premier League and FA Women's Cup. She was also a key figure in Arsenal's historic "Quadruple" season in which they won all of their trophy competitions, including the 2006–07 UEFA Women's Cup. Arsenal were the first ever British side to win the competition, with Scott scoring the only goal in the two-legged tie with Umeå IK. She appeared in 22 Premier League games, scoring two goals. In all competitions, she made 40 appearances and scored four.
The 2007–08 season saw Scott appear in 21 games, scoring once. In all competitions, she made 35 appearances, scoring three goals. In 2008–09 Scott scored once in 13 games. In all competitions, she made 24 appearances, adding two goals.
Alex Scott playing for the Boston Breakers in WPS.
In the inaugural 2009 Women's Professional Soccer season, Scott played in 17 games (all starts, 1446 total minutes) for the Breakers. She scored one goal and added one assist. In 2010, Scott featured in 21 games (all starts, 1890 total minutes) and registered two assists. She started 14 of her 15 matches (playing 1249 minutes) in 2011. In December 2011, Scott returned to Arsenal on loan for the duration of a three match pre–season tour of Japan.
In 2011 Scott started 'The Alex Scott Academy' in partnership with Kingston College and Puma, for female footballers aged 16–19 years old. This represented the first such academy in the UK and was intended to highlight the growth of the women’s game. Scott also writes a weekly women's football column in the Morning Star newspaper.