Abstract Heat resistance of spores is affected by many factors such as temperature, pH, water activity (aw) and others. Previous studies have reported that free fatty acids can affect the germination and growth of bacterial spores. In this study, we investigated the influence of free fatty acids in heating medium or in recovery medium on the heat resistance of spores of Bacillus cereus NTCC 11145 and Clostridium sporogenes Pasteur 79.3. Four free fatty acids were studied: palmitic, palmitoleic, stearic and oleic acids. During thermal treatments, the impact of these FFA in heating media was generally low, but the presence of free fatty acids in the recovery medium highly decreases bacterial spore apparent heat resistance, particularly with unsaturated fatty acids. A mathematical model was developed to describe and quantify the influence of free fatty acids in recovery media on the D-values. The z′ FFA parameter values which quantify the impact of free fatty acids were determined. The variation of this parameter value according to the free fatty acid type was compared with MIC value variation given in the literature. The model enables the decrease in D-values in the presence of free fatty acids to be estimated. The high concentrations of free fatty acids in liver or canned duck may explain the microbial stability with low sterilization values applied.