This study determined the effect of relative humidity (RH) on the survival kinetics of Salmonella enterica in tree nut flours during long term storage. Three types of tree nut (almond, chestnut, and hazelnut) flours were seed inoculated with Salmonella (3-strain) to achieve about 8 log CFU/g and stored at different RH (25, 45 and 70%) conditions under ambient temperature (21 ± 2 °C) storage for up to 120 days. Samples were analyzed at regular intervals (0, 7, 14, 21, 30, 60, 90, and 120 days) to determine the survivors on both selective and non-selective media. Salmonella populations were declined by 2.28–4.68 log CFU/g on the tested flours during the storage period. Compared to RH 25%, 70% showed a significant (P ≤ 0.05) decrease in Salmonella survival. Type of flour was found to have a variable effect on the survival of Salmonella. After 120 days of storage at 70% RH, reductions were higher on hazelnut followed by almond and chestnut flours, respectively. Bacterial population decline was found to be higher during the first 60 days of storage at 25 and 45% RH. At the same time, cell viability decreased most between 60 and 120 d in hazelnut and almond flour at 70% RH.