The right-back has signed a contract with the Rojiblancos that runs until 2017, with the deal between player and club arriving two days after Javier Manquillo, Oliver Torres and Koke put pen to paper on new terms.
"It's not just Juanfran's contract, Oliver, Koke, Manquillo, Diego Costa, and, a while back, [Joao] Miranda all renewed too, and [Thibaut] Courtois extended his loan deal," coach Simeone said in a press conference.
"Without a doubt the club is maintaining the structure that has allowed us to remain competitive in recent years.
"These players all feel that they belong to this club, and that's healthy for the coach too. I'm very happy because these players give the club an identity."
Atletico have won all of their three games so far this season and host newly-promoted Almeria on Saturday.
Simeone has a full squad to choose from after all his players returned unscathed from the international break, although new signings Toby Alderweireld and Josuha Guilavogui have been left out.
The Argentinian coach said Almeria were "a team that got promoted by scoring many goals and have some interesting attacking players".
He added: "They are strong going forward and take a lot of shots. It will be difficult for us because they defend well, so we'll need to play with a lot of intensity."
Almeria have had a dramatic return to Spain's top flight, scoring six goals and conceding seven in their three games. They have taken the lead in each match, but have taken just two points so far.
Midfielder Jesus 'Suso' Fernandez, who joined on loan from Liverpool in the summer, believes his side will have a chance of getting something from the game if Atletico underestimate them.
""Perhaps they will relax a bit against us," he told a press conference.
"It's going to be a very difficult game because of the quality of our opponents but we are playing good football and if we keep doing that then we can get a good result."
And the 19-year-old insisted he was not concerned by the fact his side are yet to win a game, adding: "We are playing very well, even though we've had back luck with our results, but that will come."