The commission said the new "beta" registration service offered a number of improvements to its previous online service, including clearer application forms, a charity name-check facility, auto prompting and completion, hard-copy printing and quicker turnaround times.
The service will also use questions tailored to different types of charities.
The new service will run alongside its predecessor for a short period until it has passed tests. Once this has been completed, the old service will be removed from use.
The Charity Commission said the new service was part of its move towards "digital by default". It already has a beta search tool, which has been in operation since March 2015.
Stephen Grenfell, head of registration at the commission, said in a statement: "We want to create a smooth and intuitive experience for all those who use our service. Given that we receive on average 680 new applications for registration each month, we’ve designed the service to make our work more efficient, as well as improving the experience our customers have.
"We’re also encouraging customers who have started applications using our existing service (and not yet completed them) to finalise and submit them in full. Or better still, start a fresh application using the new service."