Rea travelled to London to meet with his wife Tatia and his parents Johnny and Claire as they attended the lavish ceremony at Buckingham Palace.
The Duke told the 30-year-old Northern Ireland rider how his love of motorcycles had been put “on the back-burner” because of his growing family.
Rea made history this season as he became the first rider ever to win the World Superbike title three times in succession.
“I know he’s a bit of a motorcycle fan himself,” Rea said.
“We talked about his bikes and the fact that he has put it on the back-burner a little bit because of his children now.”
Along with his brother Prince Harry, the Duke has been a keen biker from a young age and had previously been known to own bikes including a 1199cc Ducati and a 600cc yamaha trials bike.
Reflecting on a special day for the Rea family, Jonathan said: “It was an incredible experience to receive the MBE today from The Duke of Cambridge. The ceremony at Buckingham Palace was so nice and something I will remember forever.
“To be with so many other amazing people, in those surroundings, receiving their own Honours was really special. Being awarded this award outside of my sport it’s makes me so proud of what I have achieved and to also be held in the same esteem as Joey Dunlop and Carl Fogarty means an awful lot to me.
“I was really lucky to be joined by my wife Tarsh and Mum and Dad in the audience to witness the presentation,” he added.
“They have been so supportive of everything I have done and achieved so I am super happy that they can be part of this day as well.”
Rea won in Qatar at the start of November to end the Superbike season with 16 victories, 24 podiums and a total of 556 points, surpassing 2002 champion Colin Edwards’ previous record haul of 552.
The Kawasaki rider wrapped up his third successive title at Magny-Cours in September.