In his only season at Sealand Road, John became a fan favourite, finishing as the club's top scorer with 20 goals in 44 league games.
The rumor, however, of a fall out with manager McGrath only intensified with Thomas being dropped several times during the season to be replaced by the likes of Nigel Jemson, Frank Worthington and Steve Taylor.
[5] He was club top-scorer in both seasons, scoring 31 times in 73 games before deciding in July 1989 to sign for his boyhood heroes West Bromwich Albion on a free transfer.
John however spent the majority of his short stay at The Hawthorns on the bench, managing 1 goal in 19 games, although he did score a hat-trick in a 5–3 victory for the Baggies in a Football League Cup tie against Bradford City at Valley Parade.
After signing for £50,000 and helping North End to avoid relegation, hopes for the following season were high but were dashed by a broken leg on his return to Bolton Wanderers.
After recovering from his injury, John Thomas struggled to reach the same level again, and after just 27 more games and another six goals, he was transferred to fellow Division Three side Hartlepool United in March 1992.