Naylor played a key role in Ipswich's promotion pushes in 2003–04 and 2004–05 where the club would lose in the semi-finals to West Ham United and went on to become a staple for club in the less successful 2005–06. In 2006, Joe Royle left Ipswich and Naylor's former teammate Jim Magilton took over as manager. On 1 September 2006, he was given a testimonial at Ipswich for 10 years as a professional at the club in which 10,000 fans attended the game at Portman Road to see the current Ipswich team play against the Wembley 2000 XI. It finished 3–3 with Naylor fittingly scoring a last minute penalty. Naylor remained in the first team at Ipswich playing at the back alongside team captain Jason DeVos in 2006–07 and 2007–08. In 2008–09 his last season with the club, he was made club captain. On 14 January 2009, Naylor joined his boyhood team Leeds United on loan from Ipswich. The move was made permanent on 2 February when he joined on a free transfer. Naylor was appointed vice-captain of the club and scored his first goal for the club in the 2–0 win over Southend United. Naylor helped rejuvenate Leeds' form after signing for his boyhood club, who had previously conceded several goals from set pieces. Leeds' defence considerably improved, and when Sam Sodje also signed for Leeds on loan they made a formidable centre back partnership at the back, after Leeds had previously had some defence problems. The performances of Naylor and Sodje helped Leeds reach the playoff semi-finals, but they eventually lost out to Millwall after losing 2–1 on aggregate over two legs. Ian Westlake had revealed in the October/November 2006 issue of the "Leeds, Leeds, Leeds" magazine about Naylor that "Bam-Bam's a massive Leeds fan – he's got the white rose tattooed on his arm and sings 'Marching On Together' in the shower after training". In July 2009, he signed for Leeds permanently from Ipswich Town and Naylor was appointed the new permanent captain of Leeds United following former captain Frazer Richardson's departure in the summer. Naylor has had an operation on his back and has missed all of the 2009–10 pre season and has missed several of Leeds games in League One. During his absence the captain's armband was temporarily passed to Jonny Howson. Naylor made his comeback from injury playing 61 minutes in Leeds United's Reserves 2–1 win over Middlesbrough Reserves.