The 27-year old right-back, who joined Boro from Arsenal in 2008, was being linked with a summer move away from the Riverside Stadium but has ended any speculation by putting pen two a fresh two-year deal.
"It's great to get everything signed and now I can concentrate on the new season," Hoyte told the club's official website.
"We have a lot of new faces and there is a great atmosphere in the dressing room. There is competition throughout the whole squad and that will drive everyone on to do well.
"Middlesbrough is a fantastic club and I have really enjoyed my time here. The North East is now my second home and I feel very settled in the area.
"I really believe we can make a strong challenge this season and I'm looking forward to playing my part."