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.

The accusations come via a formal complaint in the US by consumer groups.
They, along with several EU bodies, are calling for investigations into the manufacturers.
Genesis Toys, which makes the products, has not responded to a request for comment.
Nuance Communications, the firm that provides speech recognition software for the products, said it takes data privacy seriously.
The firm is a subject of the US complaint, filed with the Federal Trade Commission, but said it had "adhered to our policy with respect to the voice data collected through the toys referred to in the complaint".
"Nuance does not share voice data collected from or on behalf of any of our customers with any of our other customers," spokesman Richard Mack said.
In addition to the data protection concerns, a hack allowing strangers to speak directly to children via the My Friend Cayla doll is still possible.
The Norwegian Consumer Council also assessed the toys and their terms and conditions. They found the products lacking and potentially in breach of advertising regulations.
"It's quite disturbing because the company reserves the right to direct marketing towards kids," said Finn Myrstad, technical director of digital services at the council.
In January 2015, the BBC and security researcher Ken Munro, at Pen Test Partners, revealed the vulnerability in Cayla's software that allowed the doll to be hacked.
And Mr Myrstad said it appeared the problem had not yet been fixed, nearly two years later.
According to the US complaint, the doll prompts children to provide personal data verbally - including their parents' names, the name of their school and the place where they live.
It also says the toys allow unauthorised Bluetooth connections from any phone or tablet within 50ft (15m).
The Norwegian Consumer Council has now filed its own complaints to three authorities in Norway, including the consumer protection ombudsman.
Further complaints from other bodies are to be filed in France, Sweden, Greece, Belgium, Ireland and the Netherlands.
Mr Myrstad added that he was concerned the manufacturers also reserved the right to change the terms and conditions at any time.
"We think this is particularly worrying because we're dealing with recordings of voice - kids' data," he told the BBC.
"How the data's collected how it's stored and shared - all of that appears to be almost entirely unregulated," said Rik Ferguson, a researcher at security firm Trend Micro.
"And the parents are certainly not made aware in any comprehensible fashion of the extent of data that's collected or how it may be used in the future."
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.
[NEXT_CONCEPT]
The makers of the i-Que and Cayla smart toys have been accused of subjecting children to "ongoing surveillance" and posing an "imminent and immediate threat" to their safety and security.