A fit again Fuller began the 2003–04 season on fire, including a run of six goals in five games, but his form tailed off as his knee troubled him once more. Despite this, he still scored 19 goals that season.
Fuller failed to make a huge impact in the Premier League, falling down the pecking order as the season progressed. Despite the sale of some of his fellow strikers at the end of the season, the return from long-term injury by strikers Vincent Pericard and Svetoslav Todorov, and the purchase of Collins Mbesuma, meant Fuller was not guaranteed first team football at Portsmouth and new manager Alain Perrin agreed to let Fuller go. A move to Sunderland fell through when Fuller failed a medical. Instead he was re-united with Harry Redknapp, who signed him for Southampton for £90k.
In February 2006, he went on loan to Ipswich, where he had an eventful time. In four games, he scored two goals, collected two yellow cards and one red card in the 2–2 draw at Crystal Palace (one of his former clubs), for a hand gesture at the crowd. He returned to Southampton at the end of March.
On his return to Southampton, he was a changed player and in the final six games of the season he scored six goals to bring his tally for the season to nine. Unfortunately, he didn't fit into George Burley's plans for 2006–07 and was transferred to Stoke City on transfer deadline day, 31 August 2006.
In the 2007–08 season, Fuller weighed in with 15 goals including a hat-trick against West Bromwich Albion at the Britannia Stadium. He has also seemingly controlled his discipline further this season becoming a firm fan favourite in the process. Fuller missed Stoke's home game against Hull City as he was attending the funeral of his grandmother in his home nation of Jamaica.
Fuller scored Stoke City's first-ever Premier League goal, a late consolation in a 3–1 defeat to Bolton Wanderers on the opening day of the 2008–09 season. He followed this up with a fine individual effort in Stoke's 3–2 win over Aston Villa F.C. in their first ever Premier League home match. This goal won "goal of the month" for August.
|-
|2000-01||Crystal Palace||First Division||8||0||colspan="2"|-||colspan="2"|-||8||0
|-
|2001-02||Heart of Midlothian||Premier League||27||8||2||2||colspan="2"|-||29||10
|-
|2002-03||rowspan="3"|Preston North End||rowspan="2"|First Division||18||9||colspan="2"|-||2||2||20||11
|-
|2003-04||38||17||2||2||1||0||41||19
|-
|2004-05||Championship||2||1||colspan="2"|-||colspan="2"|-||2||1
|-
|2004-05||Portsmouth||Premier League||31||1||2||0||4||0||37||1
|-
|2005-06||Southampton||Championship||30||9||1||0||colspan="2"|-||31||9
|-
|2005-06||Ipswich Town||Championship||3||2||colspan="2"|-||colspan="2"|-||3||2
|-
|2006-07||Southampton||Championship||1||0||colspan="2"|-||1||0||2||0
|-
|2006-07||rowspan="3"|Stoke City||rowspan="2"|Championship||30||10||2||1||colspan="2"|-||32||11
|-
|2007-08||42||15||2||0||colspan="2"|-||44||15
|-
|2008-09||Premier League||6||3||||||||||||203||64||9||3||8||2||220||6927||8||2||2||colspan="2"|-||29||10230||72||11||5||8||2||249||79
|}