Bolton, under the guidance of Phil Neal, finished the 1990-1991 season off in fourth place, a fantastic position that saw them reach the play offs however crashing out in the final. They enjoyed a fine run in the FA cup that saw the club reach the fourth round of the competition, meeting defending cup winners, Manchester united, narrowly losing the cup tie 1-0.
The 1991-92 season saw the Trotters stumble in the third division, finishing the campaign off in a mid table finish of 13th position. They did however enjoy a fine FA cup run, which saw the club reach the fifth round of the competition, meeting top flight club, Southampton. Bolton held the side to a replay which they narrowly lost 3-2 in what was a heroic performance by the Trotters.
The 1992- 1993 season was a mighty success for Bolton as they finished the campaign off as runners up in the third tier of English football in second place. Mark Patterson, Alan Stubbs, John McGinlay and David Lee were all in outstanding form for Bolton during the campaign. The Trotters once again were outstanding in the FA cup, reaching the fifth round of the competition for the second successive campaign. This time they lost 3-1 against Derby County in a hard working encounter.
The 1993- 1994 season was a fine one for Bolton Wanderers as they finished the season off in 14th place in their first season back in the second tier of English football for eleven years. They enjoyed their finest FA Cup run in 35 years as they reached the quarter finals of the competition, suffering defeat against Oldham Athletic in the last eight.