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
1896–97 Thames Ironworks F.C. season even though the West Ham area was still officially part of Essex at the time. It was a seamless transition for the club to make as Thames Ironworks and Shipbuilding Co. Ltd owner Arnold Hills was also president of the London League, and along with Thames Ironworks F.C. committee chairman Francis Payne, helped to draft the competition's rules. New signings for the season included Reading players Edward Hatton, Peter Davie and Frank Dandridge. H. Rossiter and Holmes, would also join from the Berkshire club, as well as many more Thames Iron Works employees that still provided the core of the