The 22-year-old, who joined on a free transfer from Barcelona last summer, found first-team opportunities limited at the start of the campaign, but eventually became more of a regular fixture in defence and started the club's final four games.
It was also Hughes' debut season at the Britannia Stadium after six months out of football and he led Stoke to their highest Premier League finish in ninth.
His predecessor, Tony Pulis, was often the subject of criticism as he was accused of playing long-ball tactics despite managing to establish Stoke in the top-flight.
Muniesa was full of praise for Hughes and says that the style of football he has implemented is not too dissimilar to that from his time at the Nou Camp.
"It is Stoke's highest finish and I have had a great experience with many great memories of my part in games," he told Catalan radio station RAC 1.
"The way of playing is easy. We have had five years of playing in the same way with the long ball, but under Hughes we have tried to change that style and be more like Barca.
"The Premier League can be physical though and occasionally we have ended up returning the to the long-ball system."
Meanwhile, Muniesa also praised Barcelona captain and former team-mate Carles Puyol, who is set to play his final game before retiring in the La Liga title decider against Atletico Madrid.
"To me he is an idol," said Muniesa.
"He is one of the best defenders Barca has ever had and the captain of the best Barca team in history.
"Also, he is an exceptional person who has always been fantastic with me and I always will be grateful for that."