David Silva opened the scoring after just three minutes to leave Boro fans fearing a rout.
To their credit, Aitor Karanka’s side rallied and missed fine chances to equalise through Cristhian Stuani, Rudy Gestede and Marten de Roon.
City made them pay and after Brad Guzan had thwarted the Blues several times on what could be his last Boro appearance, Leroy Sane crossed for Sergio Aguero to kill off the sixth-round tie on 67 minutes.
City have stretched their unbeaten run to 11 games and they will head into Wednesday’s Champions League return with Monaco in confident mood.
Here are five things we learned:
1) Pep’s heading back to Wembley
Wembley is dear to Guardiola and he was part of the Barcelona team which lifted the European Cup for the first time there in 1992 when Ronald Koeman’s goal beat Sampdoria.
He was back in 2011 to mastermind Barcelona’s victory over Manchester United in the Champions League Final.
The Spaniard says he has always been captivated by Wembley and now he will have the chance to lead Manchester City out there in the FA Cup semi-finals.
2) Manchester City can’t stop scoring in the FA Cup
The City slickers were the top scorers after the fifth round and their double against Middlesbrough took their tally in the competition to 15.
David Silva opened the scoring with a left-foot finish and the Spaniard has been involved in five goals in his last five FA Cup games. He has two goals and three assists to his name.
City possess such offensive power in him, Sergio Aguero, Raheem Sterling and Leroy Sane. Thirteen of those goals came in just three games and they are a nightmare for defences.
3) Claudio Bravo still doesn’t impress
Bravo started for the first time since being targeted by some City fans who booed him sarcastically for his display against Huddersfield in the fifth-round replay.
He did not look convincing early on against Middlesbrough and fumbled a header from Rudy Gestede. Luckily for the Chilean, Pablo Zabaleta was beside him to hoof the ball away and clear the danger.
Bravo did improve, but it’s still hard to fathom why Pep Guardiola bombed Joe Hart out of City to sign him.
4) Mike Dean appeared to let the City players influence his decision making
Antonio Barragan fouled Leroy Sane in the first half and it was only when the City forward refused the Boro defender’s hand in apology that Dean decided that the challenge was worth a booking.
Dean was at it again in the second half when John Stones tussled with Alvaro Negredo. Negredo did give Stones a tug as he vied for the ball, but Dean only blew for a foul when Stones stopped playing and appealed for the decision.
5) Brad Guzan signed off on a high
Guzan excelled in what could be his last appearance in England before he heads back home to the US at the end of the season.
Guzan has agreed to join MLS side Atlanta United and the American turned on the style in what could be his final game for Boro.
Guzan stopped Manchester City turning this FA Cup tie into a rout as he made fine saves to deny David Silva twice, Sergio Aguero and Leroy Sane. His stop from Aguero stood out as he deflected his goalbound shot onto the far post.