Sweet cherries are highly perishable fruit, consequently postharvest treatments are indispensable if longer shelf-life is desired. The use of synthetic fungicides is getting more and more repudiated, generating the demand for new sustainable and gentle “natural” sanitation techniques such as fumigation with acetic acid (AA). Not least due to still existing technical problems and lack of knowledge of basic mechanisms of action and interactions between the various intrinsic and extrinsic factors this technique has not been introduced into practice. Therefore, the efficiency of AA fumigation at three different concentrations and two practically relevant storage temperatures was analysed on the cultivars ‘Merchant’ and ‘Oktavia’. Even low AA vapour concentrations (3 mg L−1) reduced mould counts to near the detection limit, while low temperature storage can delay (‘Merchant’) or prevent (‘Oktavia’) mould regrowth. Higher AA vapour concentrations (>3 mg L−1) sustainably reduced yeast counts during storage at 4 °C. AA vapour treatment moderately and temporarily decreased bacteria counts. Efficiency of AA fumigation varied between both ‘Merchant’ and ‘Oktavia’ cherries. AA fumigation can be, in particular, helpful against mould-caused spoilage in fruit of both cultivars. For highly efficient treatments minimum AA concentration of 6 mg L−1 is recommended.