The housing thinktank appointed the office over three other shortlisted practices, Hawkins Brown, Conran & Partners and Richard Partington Architects.
Cole Thompson Anders' designs for a cluster of six new homes will be built on a small site in the 'garden village' of New Earswick, York.
The Suburban Homes competition judges praised the scheme for 'combining strong, visual appeal with an impressive degree of attention to environmental standards and sustainability'.
The Rowntree Foundation said that these 'prototypes' should provide 'inspiration and ideas' for Derwenthorpe, a planned mixed-tenure development of 540 homes in the east of York.
Rowntree director Richard Best said he was delighted with the competition's result.
'We were not sure if our demanding criteria could be met, so we were delighted that Cole Thompson Anders has designed a building complex that seems destined to fulfil all our ambitions for the site,' he said.
'The development reflects the distinctive architecture of the neighbouring 'Folk Hall' community centre and complements the houses around it.
'The appearance should add appeal for purchasers, yet the actual building costs should ensure affordability for tenants and part-purchasers,' he added. 'It also contains impressive, state-of-the-art eco-features to take forward the sustainability agenda.'