Although Jones did not have to think long about stepping into Steve Round's shoes, he admitted that it was not easy to end his eight-year association with the Latics.
However, he and Martinez are now looking forward to the new challenge with the Toffees.
"It wasn't a difficult decision to join Everton but it was a difficult decision to leave Wigan because I had four years there as a player and four years there as assistant manager," the 43-year-old told evertonfc.tv.
"You have a certain attachment to any club - if I have eight years at Everton it would certainly be difficult to leave. You meet good people but we felt like the time was right, the opportunity was right and we took it. We are ready to go.
"It is the next step for us and it's a huge club with huge tradition. You notice the great standards straight away when dealing with the people in and around the club. The club motto (nothing but the best) certainly rings true."