Although considered by most as the "Patriarch" of Panathinaikos, Nikolaidis was responsible for one of the biggest crises in the history of the club, the breakaway 1931. While he was a leading board member of the club, he had a major dispute with Angelos Messaris, the best player of the team. The dispute 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. It was rumoured that Nikolaidis was involved in Messaris' application being rejected three times by NTUA. This dispute led Messaris to quit football altogether, much to the dismay of a significant number of players and administratives, who sided behind Stamatis Merkouris, the son of Athens' Mayor at the time. Merkouris challenged Nikolaidis' authority, eventually leading to a poll. Nikolaidis won by a small margin and he immediately ousted from Panathinaikos all those who stood against him, including a figure with mythical proportions to PAO fans, the founder of the club Giorgos Kalafatis. Although many of them joined the team again later, this action was never forgiven by a portion of the fans.