The two bosses clashed on numerous occasions before Guardiola stepped down as Barcelona boss last summer, after losing out on the Liga title to Real Madrid.
Deco himself enjoyed four years at Camp Nou between 2004 and 2008, but despite his links with the Catalans, he has offered his backing to his compatriot.
“Winning in all places as Mourinho has done is harder,” he told RTP.
“Guardiola is a great coach, but Barcelona went on to say that he did not invent anything. But let’s see how he does with other teams and different training methods, then we can make a better assessment.”
The Fluminense man also had his say on Cristiano Ronaldo and Lionel Messi, with the pair hot favourites to lift the Ballon d’Or and admits he finds it impossible to separate the two.
“During this year Cristiano was the best player in the entire first half and now it is Messi who is doing amazing things. I do not know who will win, honestly it’s hard, ” he added.