The blaze is the latest disaster to hit the site after the steel frame failed during construction of the new £6.1m City Gates Christian Centre last Tuesday.
The London Fire Brigade confirmed that they were called to the site last Thursday night.
A brigade spokesman said: “The building had previously collapsed on Tuesday 31 January and was in the process of being demolished.”
Crew manager Jim Jobson from Ilford fire station who was at the scene said: “We worked extremely hard in what were difficult conditions as the building was very unsafe.
“We were unable to get into the building as there was a chance that bricks and other materials could fall on crews. Firefighters were at the scene throughout the night and contained the fire to the collapsed building.”
Four fire engines and around 20 firefighters were called at 0012. Crews from Ilford, East Ham and Stratford were at the scene. The cause of the fire is under investigation.
Main contractor on the job is Ashe Construction and the steel frame was built by Norfolk based DGT Structures.
The HSE is currently investigating the cause of the original collapse.