Gov.uk is designed to cut down on the number of different sites offering government information and services. It covers a range of subjects and includes information from non-departmental government bodies.
The commission last year asked for an exemption from being part of gov.uk because it said it needed to maintain its independence from the government, but this request was turned down.
A commission spokeswoman said this week that the regulator had since been assured that it would not be expected to adopt government branding when it joins the site "in the next year or so".
"We have had several meetings with the Government Digital Service, which has now been able to talk us through how things would work practically," she said. "Most importantly, from the perspective of our independence, we have been given an exemption from having to adopt the standardised government branding.
"This means there will be clearly branded commission content on gov.uk, which will link back to services on our own website."
Gov.uk would include information from the commission that is more relevant to the public, she said, and the commission’s site would contain more corporate information.
The commission is due to update its own website for a launch this month. The updated site will feature a redesigned home page that prioritises the information that is most commonly searched for on the site, such as founding a charity, registering with the commission and changing a charity’s details.
The site will also include short summaries of commission guidance, linked to the guidance itself, to make it more accessible.