The Commission suspended the website on Friday, after installing an interim manager to deal with serious financial problems.
Online giving has become popular because of the ease of donating, simply through the click of a mouse.
However, it appears that a major shortfall appeared in recent weeks at charitygiving.co.uk, between the sums donated and the money passed on to charities.
The site had been handling donations of around £100,000 a week.
The Charity Commission believes that thousands of people staging charity runs and other events could have been affected.
In a statement it said: "The interim manager will now undertake an urgent, detailed review of the charity's finances to establish the extent of the shortfall and which charities and donors are affected."