Although considered by most as the "Patriarch" of Panathinaikos, Nikolaidis is involved also in one of the biggest crises in the history of the club, the breakaway of 1931. While he was one of the leading board members of the club during the presidency of Nikolaos Xiros, he had a major dispute with Angelos Messaris, one of the best players of the team. The reasons of the dispute were not clear, but maybe was about Messaris wanting to study engineering at the National Technical University of Athens, while Nikolaidis did not want him to be involved in anything except football.
The bad situation led Messaris to quit football altogether, much to the dismay of a significant number of players and officials, who sided behind Stamatis Merkouris (son of Spyridon Merkouris, Athens' Mayor at the time), also member of the board. Merkouris challenged the team's authority, eventually leading to a poll. Xiros and Nikolaidis won by a small margin and the new board immediately ousted from Panathinaikos all those who stood against, including a figure with mythical proportions to PAO fans, the founder of the club Giorgos Kalafatis. Although many of them (including Kalafatis) joined the team again later, this action was never forgiven by a portion of the fans.