The men's monthly launched in December. It conducted research with 500 readers to improve users' experiences with the magazine for its ninth issue.
The magazine is now using more HTML, has scrapped several flipping-page features and is extending tabs to focus more on the magazine's overall look.
Virgin Digital Publishing said its survey found more than 70% of readers use Project to showcase their tablet.
Basil Hassan, head of business development at Virgin Digital Publishing, said: "Issue nine showcases our new streamlined user interface and navigation, based on reader research and in-depth analysis of user behaviour, to maintain our position as 'The Magazine for iPad' and the future of digital publishing and advertising.
"We have got this amazing new platform to deliver on and we want to make sure we deliver the best we can."
Project's creators have also designed custom-made analytics software that allows them to monitor users’ interaction with the magazine and feed this back to advertisers.
Hassan said: "One other interesting statistic from our reader survey was that over 70% of readers use issues of Project magazine to showcase their tablet, so we think this is a great platform for device manufacturers and advertisers to showcase their digital expertise."
The title is set to engage more with its readers through an upcoming creative consultation project sponsored by BMW, and says it is looking at the possibility of extending into mobile platforms.
The magazine's latest issue includes a video cover featuring Sir Paul McCartney in Chicago during his US stadium tour.
The £1.99 issue includes ads from Kronenbourg, L’Oreal, Audi, Armani and Nissan.