Manchester City had been interested in exploring a deal for the player depending on the future of Leroy Sane, while the likes of Juventus, Barcelona, Manchester United and Real Madrid had all also been linked.
But it's Atleti that have secured his signature, with sources having revealed to Goal that talks began on June 1, with the Liga club's CEO Gil Marin meeting Benfica chairman Luis Filipe Vieira during the Champions League final to kick off negotiations.
Marin then met Joao Felix in person and Atleti, with the help of Jorge Mendes, went on to convince the 19-year-old and his agent Pedro Cordeiro to travel to Madrid by way of an introduction to the club and their facilities.
Diego Simeone also played a key role in convincing Joao Felix to join Atleti having contacted the player directly, with the most expensive transfer in the club's history having now been formally announced.
Such a fee sees the teenager become the third most expensive footballer of all time behind Paris Saint-Germain duo Neymar and Kylian Mbappe, and just ahead of Barcelona midfielder Philippe Coutinho.
Widely lauded as Portugal's next big star in the making, Joao Felix has been likened to Kaka and Antoine Griezmann - who is set to leave Atleti this summer - and it has also been claimed that compatriot and Premier League champion Bernardo Silva did not show the same promise at 19.
Indeed, having already been called up to the Portugal national team despite his tender years, it would appear that Simeone and Co. are not the only side willing to put their faith in a versatile youngster who can play anywhere across the front line.
Joao Felix is the star name in what looks set to be a dramatic summer rebuild at Atletico, with Simeone reshaping his squad in reaction to the departures of key players throughout the spine of his team.
Long-serving club captain Diego Godin confirmed his exit at the end of his contract, with Griezmann having announced that he will be quitting and Rodri also informing Atleti he will be leaving ahead of finalising a move to Manchester City after the Premier League side met his release clause.
In terms of incomings to add to Joao Felix's arrival, midfielder Marcos Llorente has been signed from rivals Real Madrid, while centre-back Felipe has been brought in from Porto.