"The atmosphere at the club, and the entire squad could testify to it, wasn't good," the club's record signing told Sky Sports News on Tuesday.
"The things that we were doing, and the way that we were playing football, it was not encouraging for a lot of us."
Welshman Pulis, who led Stoke into the Premier League but was criticised for his abrasive style of football, left the club by mutual agreement in May.
"You would probably not have seen a lot of the players at the club if the situation had remained the same," said Jones.
In May, Jones found a pig's head, reportedly left by players, in his locker. Media reports said he retaliated by using a golf club to smash the windscreen of a car belonging to Ireland midfielder Glenn Whelan, but later apologised. The club promised an investigation into the incident.
Jones praised the changes that Mark Hughes had made since replacing Pulis, and said Stoke could finish in the top half of the Premier League this season.
"At the moment I am happy with the way that we are working every day. It's been wonderful since the new manager and new team came in.
"Now I'm confident that we can do well this season and will probably finish in the top 10," added Jones, whose contract expires at the end of the season.
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