Three fire crews were called to Waste4Fuel just before 5am on Tuesday.
Two machines from Sidcup and one from Orpington rushed to the scene in Cornwall Drive after receiving several calls of smoke coming from the plant.
Crews found a number of small fires within the pile, to assist the owner in dealing with these crews used two jets to put the small fires out.
Richard Welch, Bexley borough fire commander, told News Shopper: "We are doing all we can, working in partnership with the owners and many other agencies to ensure that the issues with this site have minimal impact on the local residents and business community.
"These fires were not suspicious."