Jimmy Nicholl of Raith Rovers was named as McCarthy's replacement, but could not control the slump in form which witnessed Millwall demoted at the end of the season in 22nd place. Just five months before this they had been top of Division One looking for a place in the Premier league. Instead Millwall discovered themselves in Division Two for the 1996-97 season. The club also experienced extreme financial difficulties that saw them being placed in financial administration for a short period of time. Jimmy Nicholl was relieved of his duties and John Docherty came back on a short term basis to stabilise the team at playing level.

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The club came out of administration, and new chairman Theo Paphitis appointed ex-West Ham United (Millwall's bitter rivals) manager Billy Bonds as manager. Paphitis proposed that Millwall should play in grey shirts, but after considerable pressure from fans groups, he relented and Millwall's home colours became all white, with a blue away strip. He also dispensed with the Roaring Lion crest, replacing it with, in his words, "a less aggressive emblem". An ongoing campaign was launched to have the Roaring Lion restored to the Millwall Shirt. This was not a successful season, with the club moving close to relegation to the Third Division. Bonds left and replaced by the long-serving and popular Keith "Rhino" Stevens, with Alan McLeary as his assistant. McLeary was promoted to joint manager.