The regulator opened a compliance case earlier this year after receiving a serious incident report from the charity that brought up concerns about the treatment of staff and the behaviour of a senior manager, it has emerged.
In a statement, Refuge said it had made changes to how the charity was governed in response to the allegations.
"A complaint was received against the charity," the statement said. "The trustees took immediate action and arranged for it to be independently investigated.
"Following the investigation, some changes have been made to governance structures. The Charity Commission was satisfied with the action taken and the case is now closed."
In a statement, the Charity Commission said the charity had responded to its concerns and made changes including "increasing trustee presence within the charity, reviewing a number of their policies, implementing a framework of organisational values and reviewing staff workloads".
Reviews of Refuge at the workplace rating website Glassdoor, where the charity is rated at 2.1 out of five, highlight the allegedly high workload at the charity.
One review cites a high workload with a culture of unpaid overtime. Others say that staff have been undermined by senior management and micromanaged.
The Charity Commission’s statement said: "The commission opened a compliance case into Refuge in early 2018 after receiving a serious incident report from the charity regarding concerns about the treatment of staff members and the behaviour of a senior staff member.
"The trustees took appropriate action by reporting this to the commission and appointing an independent investigator to carry out a full investigation into the issues raised. We sought further information from the trustees about their general governance and how the charity safeguards and supports its staff."