Men armed with machetes raided stores in Mobberley and Macclesfield on Sunday night, shortly before they were due to close, before fleeing with cash.
In each case the robbers were wearing dark clothes and balaclavas, and detectives investigating the raids believe they could be connected.
A Co-op spokesman said no-one was injured in the robberies, but staff were left shaken.
The first robbery happened at 9.18pm at the Ivy Meade Co-op in Ivy Road, Macclesfield.
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