Thames Ironworks F.C. resigned his post as club secretary. He was replaced in the position by Irons defender George Neill, thus beginning a history of the team appointing from within. Thames Ironworks lost their first fixture in the Southern League Division One 1–0 away at Reading on 16 September 1899, but managed their biggest league win of the season only two days later with 4–0 home win against Chatham Town. Thames Ironworks recorded their biggest win of the season, in the fourth qualifying round of the FA Cup on 28 October, trouncing Dartford away 7–0. However, The Irons good form soon ended on
Thames Ironworks F.C. Joyce claiming his third hat-trick of the season at his former stomping ground. Thames Ironworks had survived their first season in the top division of the Southern League. In June 1900, club chairman Arnold Hill's Thames Ironworks and Shipbuilding Company acquired another engineering firm in a financial takeover and became a limited company for the first time. 4,000 ten shilling shares (50p) were sold to Iron Works staff and the general public, with Arnold Hills generous enough to match sales of any shares one-to-one. At the end of June, Thames Ironworks F.C. resigned from the Southern League and were officially