Royal Borough of Greenwich councillors resolved to refuse permission for the Charlton Riverside scheme at a committee meeting in July, contrary to an officer recommendation for approval.
Developer Rockwell Property had applied to build 771 homes in 11 buildings ranging from two to ten storeys in height.
The application proposed 292 affordable homes, 38 per cent of the total housing, and demolition of the site's existing buildings, which include a recording studio and a manufacturing facility.
In its reasons for refusal, Greenwich Council said the height, massing and design of the buildings would result in "overdevelopment of the site".
The council also said the plans failed to meet several local plan requirements, including those relating to loss of employment floorspace and the proportion of family-sized housing.
Khan called in the plans for his own determination in August.
A GLA report on the application, published yesterday, had recommended that the plans be approved.
It said the draft London Plan defines the 2.5 hectare site as a non-designated industrial site and it contains a mix of commercial, industrial and sui generis uses.
It went on to say the "design and layout principles are well-considered and the scheme achieves a high quality of placemaking, with well-defined new public routes and spaces, enhanced by high quality landscaping".
GLA officers added that "the massing strategy responds to the site characteristics and the existing and emerging context."
"The quality of design, architecture and materials will ensure a distinctive and high quality development which will contribute positively to the regeneration of this part of Charlton Riverside," the report said.
With regards to the concerns flagged by the council regarding overdevelopment, the report said the "geographical characteristics of the application site, in that it is currently accessible from the existing highway and pedestrian network and served by convenient access to existing bus and national rail services, appropriately justify the proposed divergence from the [council’s Charlton Riverside supplementary planning document] height and density guidance in this case". This "would not necessarily be supported on other sites," GLA officers added.
Furthermore, the report said, the proposed development "will kick start the delivery of the new east-west transit route which provides a significant contribution to aiding the sustainable regeneration of the Charlton Riverside and optimising wider housing and employment delivery."
But Khan went on to refuse the application.
A spokesman for the mayor of London said: "The mayor rejected this application because he believes the plans are not of sufficient design quality, the layout and massing would create an unattractive residential neighbourhood, and that insufficient consideration has been given to the impact on existing local businesses."
The mayor’s full detailed reasons for refusal have not yet been published.
Earlier this month, the Royal Borough of Kensington and Chelsea launched a legal challenge against Khan over his decision to call in plans for a new 30-storey hotel that the council had provisionally refused over height concerns.