The proposal for the 250-home scheme in Burnt Oak Broadway was turned down by Barnet's planning committee despite council officer support for the 3.5ha development.
The decision comes less than eight months after Thompson's similar proposals for 289 new properties on the site next to the new hospital were also rejected.
Masterplanned by Barton Willmore and backed by Taylor Woodrow, the latest plans would have seen 43 new houses, five nine-storey apartment blocks and a doctor's surgery built on the land.
However, the planning committee was not convinced by the designs and criticised the 'height and bulk' of the buildings - in particular the size of the apartment towers compared to the surrounding buildings and the hospital.
There were also fears about the 'overdevelopment of the site' which could be 'detrimental to the character, appearance and visual amenity of the locality'.
It is understood the development team has already restarted negotiations with the planners about the future of the project.