The club were unable to repeat their success in the FA Cup and were eliminated in the First Round, but compensated for this failure by claiming the Southern League title for the fourth time in five seasons.

The run to the FA Cup Final in 1900 had generated a surplus of £31 but the club were still £1,000 in debt. In July 1900, the company made a call on its shares in an effort to raise cash. The response to the call was disappointing with many shareholders having their shares forfeited as a result of their failure to pay the balance due.

The financial situation worsened in 1900–01, with the gates dwindling following the doubling of the entrance fees the previous year from sixpence to a shilling, and the club generated a loss of £740.

After the disappointing end to the previous season and the embarrassing failure in the FA Cup Final, there was a "drastic" clear-out of players. Both the players at the centre of the dispute surrounding the team selection for the final, Roddy McLeod and Jack Farrell were released, as were defenders Meehan, Durber and Petrie. Another significant departure was Alfred McMinn who resigned as a director; McMinn had made a major contribution to the club's success, particularly with his ability to spot a good player, leading the "Stoke Invasion" in the summer of 1895.

The new recruits included three players from Everton, full-backs George Molyneux and Bertram Sharp and centre-forward Wilf Toman as well as former Everton and England forward Edgar Chadwick, who would renew his partnership with Alf Milward which had been described as "the best in the league" during their time together at Everton. From local football, the club recruited two players who were to play a major role in the future of the club: Bert Lee would have two long periods with the club as a player before becoming a trainer from 1914 to 1935.Fred Harrison would remain at The Dell for seven years and become the club's main goalscorer, with 88 goals from 166 appearances.

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