The Brazilian centre-back is now widely regarded as one of the best defenders in European football following an excellent couple of seasons at the Vicente Calderon.
Interest arrived this summer, but Miranda decided to remain in the Spanish capital.
"I think that it's normal [for] footballers to leave the club when they have found success," he told AS.
"Staying at Atleti was the best for me and my family. I'm very happy to be at Atleti. I love Madrid and this is a great club."
Manchester United were one of the clubs believed to be interested.