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. Frank Taylor, Bob Allan and Fred Corbett. Former club secretary and Ironworks defender George Neill was also retained for the new season ahead. Tom Bradshaw's close friends Bill Joyce and Kenny McKay left for Portsmouth and Fulham respectively, while Albert Carnelly joined arch-rivals Millwall. The first, and only, known crest to be featured on a Thames Ironworks kit was the Union flag with Thames Ironworks initials ("TIWFC") surrounding it. The original colours of the team were dark blue due to Arnold Hills being a former student and football Blue of Oxford University, although the team used a variety of kits.