The current Chelsea manager's time in the Spanish capital was riddled with controversy, with his destructive relationship with the goalkeeper one of the biggest issues in the three-year spell.
After a long period of remaining relatively silent, Casillas has spoken at length about their relationship, revealing that it went from good to bad very quickly after controversy built around the club because of the actions of the coach and several players as their rivalry with Pep Guardiola's Barcelona intensified.
"I do respect Mourinho and he is a great coach," he said in an interview with Canal+. "At first, things were great with him and the relationship was good up until the fights against Barcelona - after that you can say things were not good enough.
"Mourinho first tried to send me a message by benching me and I reacted. It was a successful message to work harder.
"I called Xavi and Puyol to bring an end to all of the anger between the Real Madrid and Barcelona players. We were creating a bad image, but I didn't ask forgiveness of anyone. Mourinho didn't talk to me about this call before it. I don't know if it bothered him but people said that it did.
"He likes the players who are always honest with him. Sergio Ramos, Cristiano Ronaldo and I were always honest and upfront with him.
"In the summer of 2012, our relationship was good, we talked a lot, but then there was a change around Christmas. The team wasn't doing well and my relationship with Mourinho became poor. We had disagreements, but with respect."
Casillas admitted that reports from his wife, Spanish TV presenter Sara Carbonero, about unrest in the team's dressing room only made things worse as it was he who was blamed for leaking sensitive information to her.
The Spain goalkeeper continued: "Then Sara reported about problems in the dressing room and that was just an excuse to attack me - I thought she just repeated what everyone else had told her.
"Mourinho didn't say anything to me about Sara's words, but it was easy to notice a change in our relationship.
"Soon, I got injured and after two weeks I noticed the attacks. I was called a traitor and a mole. I feel it's a bit unfair to call me mole but I have to understand that and accept some people's opinions.
"It was hard to be called a mole and I like to think that neither Mourinho nor the president Florentino Perez really believed this.
"Maybe I should have spoken out about it then, but I opted to stay silent. Many have criticised me for staying silent, I think it makes you angrier than when you can speak out.
"We had a professional relationship and that is it. I decided to shut up. I’m not accusing anyone of anything or anyone of leaving bad things at the club. I didn't want to add fuel to the fire.
"Surprisingly, though, when I was injured, my relationship with Mourinho was good and we talked everyday.
"When I recovered, Aitor Karanka said Mourinho didn't feel I was competitive enough, and from here everything started again. My team-mates looked to me and they wondered why this was happening with me and not them too.
"While I was injured, I was a bit isolated. I asked to travel as I like to be with the team, I didn't not feel unwanted but isolated.
"I have the utmost respect for Mourinho but when there is one thing bothering you or one thing you don't like, you have to discuss it. We never told Florentino that we wanted Mourinho to leave. He's one of the best coaches I've had. A guy with character.
"I am speaking now to defend the moment, not what happened a few years ago, but I think I should have said something about it before now.
"It hurts me when my loyalty to Real Madrid is questioned - this club have given me everything."