Feeding scheme kitchens were plundered and toilets stripped by thieves who targeted schools over the.
McDonald's said it was ending a relationship of over 40 years as it axed Heinz from its supplier list.
"As a result of recent management changes at Heinz, we have decided to transition our business to other suppliers over time," it said.
In February US investment star Warren Buffett's Berkshire Hathaway together with Brazil's 3G Capital took over Heinz in a $28 billion deal.
That move brought Heinz closer to Burger King, which is controlled by 3G.
The change would not be a large blow to Heinz. McDonald's said it only used Heinz ketchup in two US markets, Minneapolis and Pittsburgh, as well as some foreign markets.
McDonald's said in a statement that it would work with Heinz "to ensure a smooth and orderly transition of the McDonald's restaurant business."
The company said they "are confident that there will be no impact to our business, our customers and our great tasting food at McDonald's."