The £12m January signing from West Bromwich Albion has yet to score for the Potters in nine appearances.
But Hughes told BBC Radio Stoke he is backing the 23-year-old to justify the transfer fee Stoke paid for him.
"Next season is when we feel Saido will have the maximum impact," said Hughes.
"It's always difficult coming in half-term, so to speak, during the January transfer window, but he's integrated well within the squad - there's no issues in terms of that."
After missing so much football during the 16 months between Albion turning down his move to Tottenham in August 2015 and his eventual move to Stoke, Berahino made only his fifth Stoke start in Saturday's 2-1 home defeat by Liverpool.
"He hasn't played a lot of football and is still getting up to speed, it's fair to say," said Hughes. "But these games between now and the end of the season will be invaluable in terms of him understanding what we are about and what he needs to do.
"We want to get him scoring and get him off and running - that will be good for him. Then we'll see a marked difference next season in terms of his impact."
It is now over a year since Burundi-born former England Under-21 international Berahino scored his last goal - in Albion's 3-2 home win over Crystal Palace in February 2016.
Stoke City manager Mark Hughes says that fans should give January signing Saido Berahino time to make an impact in the Potteries, and that he should be truly judged from next season.