It has made the 43 criteria more prominent on the site and is crosschecking information to ensure reviews are as standard as possible.
However, the site will not reveal the detailed questions it asks when measuring charities against the criteria.
"We don't have the resources to have lengthy debates with charities over scores," said Adam Rothwell, features editor at Intelligent Giving.
"We always said development of our reporting would be a long-term process for everyone involved. Every annual report we read, we learn something about different types of reporting we haven't seen before and we try to take this into account."
In a bid to promote transparency, Intelligent Giving has also launched a webcam that will be updated every five seconds showing everything Rothwell does in a working day.
Intelligent Giving has removed medical charity Lepra from its "top-ranked charity" list and upheld its decision to ban it from using its quality mark. The decision comes after its three-month investigation into allegations that Lepra misled a funder. Lepra denies the claim.