Goater moved to Reading on 1 August 2003. Reading chairman John Madejski described the transfer as "the biggest in Reading Football Club's history", but Goater's time there was not a happy one. Shortly after Goater's arrival, Reading manager Alan Pardew left for West Ham United, and Pardew's replacement, Steve Coppell, did not regard Goater as part of his plans. In his second and final season at Reading, Goater played just four times, and was loaned to Coventry City. Goater then considered retirement, but instead moved to League One club Southend United for a final season as a professional. The move, a free transfer, was completed on 3 August 2005. At Southend, Goater acted as a mentor for young striker Freddy Eastwood, and contributed towards a second successive promotion for "the Shrimpers", scoring 11 goals. His final appearance before retirement was on 6 May 2006, when Southend played Bristol City, one of Goater's former clubs. The crowd included an estimated 400 Manchester City fans who travelled to Southend to mark the occasion.