Barcelona players such as Andres Iniesta, Gerard Pique and Xavi had all accused the Portuguese coach of tarnishing the reputation of not only Madrid but Spanish football in general.
Mourinho failed to achieve what was arguably his most important goal and win la Decima, the 10th European Cup, but despite this and the negative publicity the 50-year-old has received, Perez is adamant Mourinho has done nothing to harm the image of the club.
“Mourinho has helped us to make a qualitative leap which is very important. I never tire of repeating, he has not sullied the image of Madrid,” he told 20minutos.
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"I always give the example of F1, Ferrari does not always win, but they are the team that everybody knows. In football, that brand is Real Madrid.”
The Madrid president also touched on the conflict between goalkeeper and coach that resulted in Iker Casillas being dropped to the bench, losing his place to Diego Lopez as los Blancos' No.1.
“There came a time when Mourinho gave a warning to Casillas, but he does so with all players," he added.
"Then came the injury to Iker; we had to bring Diego Lopez in and he won the job.
“Mourinho has not cheated anyone. He is what he is: very demanding and he justifies those demands. The club always put their faith in him and the one who best explained it has always been Iker.
“There have been some media that have used him [Casillas] to go against Mou. I am sure Iker will earn the confidence of the [new] coach through his work and his efforts, not because the media want to pick the team line-ups.
“With Mourinho we can reach many agreements, but none of them the type that does not allow him to speak. It will not change his personality.
“He criticised the forms, but not the bottom. He requires success and motivation. He has also suffered a lot of wear in these three years.
"Madrid signed Mourinho to strike a blow at the table and reclaim the place we should never have lost.”
Perez revealed on Monday that he is close to ending his search for a coach with Paris Saint-Germain's Carlo Ancelotti expected to complete a move within the next few days.