The main award went to a refurbishment at St Augustine's Roman Catholic church, an unlisted Edwardian church in Hammersmith in London.
Roz Barr Architects restored the unlisted Edwardian church.
The Duke of Gloucester and Vice President of the National Churches Trust, who trained as an architect, presented the award, together with a £500 cheque to the winners.
Luke March, Chairman of the National Churches Trust said: "This project has liberated a cluttered interior and brings new life and movement into the building. Of particular note is the collaboration between art and architecture with new sacred spaces including a new altar, confessionals, lecterns, candle stands and a daringly contemporary tabernacle."
Bethnal Green Mission Church designed by architects Gatti Routh Rhodes was highly commended. The new church is in the middle of a new urban block and includes a community centre, café and 14 flats.
There was also an award for repair and conservation architecture, which was awarded to PPIY architects for their work on St Margaret's church, Thimbleby, Lincolnshire.
The Victorian spire had been deteriorating so much that the church was threatened with closure and spire had been removed in 2013 but then rebuilt.
The award for Young Church Architect of the Year went to Alexa Stephens, the lead architect on the spire at St Margaret's church.
She received a prize of £250. The awards were run by the National Churches Trust and the Ecclesiastical Architects and Surveyors Association (EASA).
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