When Albion were only prepared to offer him a one-year contract, Taylor moved to Bolton permanently in July 1998 for a £90,000 fee. He was the Wanderers' top scorer in the 1998–99 season, partnering Eiður Guðjohnsen as Bolton reached the First Division promotion play-offs. Taylor scored twice in the playoff semi-final second leg against Ipswich Town, to help earn his team a 4–4 draw on aggregate and qualification for the final via the away goals rule. Bolton just missed out on a return to the Premiership by losing 2–0 to Watford in the final at Wembley Stadium. However, when Sam Allardyce arrived as Bolton manager in 1999–2000, Taylor found his chances limited.