The former Match of the Day host has regularly weighed in on the GOAT debate between the two superstars.
And he has always given World Cup winner Messi his backing, something which appears to have irked the Al-Nassr star.
He opened up on his relationship with the Manchester United legend this week and joked he will “get over it”.
Lineker told The Rest Is Football Podcast: “He doesn’t like me very much, Cristiano Ronaldo. I didn’t upset him by anything I said about him.
“Other than the fact I’m honest and think overall Messi’s a better footballer. He unfollowed me on Instagram. I’ll get over it.”
His comments left co-hosts Alan Shearer and Micah Richards in fits of laughter before he jokingly pleaded for Ronaldo to forgive him.
Lineker added: “I will always like him. I’ve met him a lot of times. I know he’s got the hump with me. But that’s OK.
“And on that note… Please Cristiano… give me a call. Let’s be friends again.”
The debate between Ronaldo and Messi has raged on for nearly two decades after going head-to-head for the biggest honours and accolades in football.
Their rivalry started from their Barcelona-Real Madrid days as they competed for the Ballon d’Or, with Messi claiming eight awards and Ronaldo taking five.
Ronaldo edges Messi in the goals department after netting more than 960 times, while Messi has 914.
Lineker risked the wrath of Ronaldo again last year when he named his Mount Rushmore of football and continued to talk up Messi.
And he didn’t even have a place for the ex-Real Madrid and Juventus star in his top four footballers of all time as he named Brazilian Ronaldo instead alongside Pele and Maradona.
Lineker said: “He’s [Messi] my favourite player of all time, quite simply because he’s the best player of all time, in my view.
“Even the difference between some of the real greats, you know, the Cruyffs, Zidane, Ronaldo, the fact that you can then have another level above them, quite clearly above them, is truly remarkable.
“Without his injuries, I think we’d have had Brazilian Ronaldo in that conversation.
“But unfortunately, he did, but he still did incredible things, and he was joyous. But he was out of the game for three and a half years and managed to come back and win a Golden Boot at the World Cup. I mean, really?
“So, if I had one more, if I had four, you know, the ‘Mount Rushmore’ thing, yeah, that would be my four. So, Pele, Maradona, Messi, Fenomeno [Ronaldo].”
