The former church of St Thomas close to London Bridge is to be turned into an 80-cover restaurant.
The church, which dates from 1703, ceased to be a place of worship in the late 19th century. It later served as the chapter house of Southwark Cathedral.
The building was damaged during the construction of the Jubilee line extension in the mid-1990s and placed on English Heritage's 'at risk' register.
In 2007 it was refurbished and now serves as the headquarters of property developers The Cathedral Group plc.
The Old Operating Theatre, Museum and Herb Garret occupies part of the church tower and roof space.
Now a planning application has been submitted to Southwark Council seeking the conversion of the church into an 80-cover restaurant, the provision of a new lift for access to the museum and the creation of a flat in the church tower.