The art deco building had a £4.2m refurbishment in 2013, reopening with a cinema, cafe and gallery.
But the cinema closed in March, while the pavilion closed three days a week, prompting campaigns for them to reopen.
Prof Tony Hazell, of Penarth Arts and Crafts Ltd (PACL), which runs it, said the pavilion had not been run in a sustainable way.
He said his team had opened on "full throttle" in December 2013, running the landmark building on the Victorian pier seven days a week, 12 hours a day, 362 days a year.
"It probably wouldn't be sustainable on a commercial basis, let alone a charity one," he added.
Mr Hazell said the decision to close the cinema - the only one on a pier in the UK - was taken after figures from previous years showed it did not attract as many visitors in the summer months.
In addition, the cafe was closed on Mondays, Tuesdays and Wednesdays because it was not making enough money to cover costs.
But after reviewing the business and receiving £126,000 in lottery money, he said the pavilion and its cafe would reopen either five or six days a week from the middle of the summer. It will probably remain closed every Monday.
He also said the cinema would welcome visitors again from September "if not before".
"We are now looking for new ideas about how to raise more revenue," he said.
"At the end of the day, this building is run as a charity and people don't really donate as much to a building as they might to an animal charity.
"We only have a small team of paid staff and we rely a lot on volunteers. But, yes, we will survive."
However, campaigner Andrew Jones, 52, who started a petition to reopen the cinema - signed so far by more than 1,700 people - said he did not have faith in PACL.
"There has been a complete wall of silence in Penarth from PACL," said Mr Jones, who lives in Penarth.
"The cinema shut down very suddenly, with just a notice put on their website, which not many people saw," he added.
"I certainly don't believe cinema attendances fell that much in the summer."
Vale of Glamorgan council, which runs the pier and leased the pavilion to PACL for 125 years on a peppercorn rate, said it had "provided significant amounts of both financial and professional" support to the charity.
It gave £800,000 towards the renovations - in addition to money from the Heritage Lottery Fun - and a £100,000 grant in its first year of trading to help support the group.
"Since this grant came to an end professional support has been provided by the council to help PACL improve their approach to business planning and financial management," a spokesman added.
"Having supported them to such an extent the council is keen to see the organisation flourish and to continue to provide facilities that we know are greatly valued by the local community."
Penarth Pier opened in 1895 and was voted pier of the year in 2014 by in a poll by the National Piers Society (NPS).
Fears over the future of the renovated Penarth Pier Pavilion are unfounded, the charity running it has said.