Chipperfield's scheme, which proposed the demolition of a 1920s block at 66-68 Bell Lane to make way for a new five-storey building, was turned down by the development committee at the London Borough of Tower Hamlets last week.
The new brick development would have connected to Emin's existing studio and residence, which occupies an adjacent Victorian building at 1-5 Tenter Ground, right by Old Spitalfields Market.
"Officers have concluded that on balance the scheme would have a negative impact on the Artillery Passage Conservation Area, with its demolition of a locally listed building of both historic significance and aesthetic and townscape merit," said a statement from the committee.
Emin is one of a group of contemporary artists known as the YBAs, which emerged in the late 1980s. Among her most famous artworks are My Bed and Everyone I Have Ever Slept With 1963–1995.
A number of preservation groups objected to Chipperfield and Emin's plans, citing the negative impact of a contemporary building on the Artillery Passage Conservation Area.
The East End Preservation Society referred to the scheme "very damaging", while Save Britain's Heritage claimed the demolition of the existing 1920s building would cause "substantial harm" to the conservation area.
The scheme was initially submitted for planning consideration in summer 2015, but after a six-month period of indecision Emin launched an appeal through chartered surveyor Montagu Evans in January 2016. The appeal was received days prior to the official rejection at last Wednesday's meeting and is still ongoing.
This isn't the first project David Chipperfield Architects has had turned down for on the basis of preservation. In 2013, the British firm was appointed to design a £18.9m extension for the Geffrye Museum in east London.
The addition to the interiors museum proposed the proposed the demolition of the 1830s Marquis of Lansdowne pub, which, like 66-68 Bell Lane, sits in a conservation area in east London. A campaign was mounted by conservationists to retain the then-derelict building and the plans for the museum extension were thrown out by planners at Hackney council.
David Chipperfield Architects is currently working on a museum beside the Taj Mahal, and was recently unveiled as one of the winners of a competition to overhaul sites across Paris.