The present invention is directed to an integrated system of improving nut product safety, quality and production costs. Formulations and methods are provided for reducing pathogen contamination of nuts, improving storage stability of stored nuts and reducing refrigeration costs, and enhancing shelling operations by improving the contrast between nut shell fragments and nutmeats. The formulations may be used individually or in combination to provide all three commercial benefits of reduced bioburden, enhanced storage stability, and greater sorting efficiency of nutmeat from shell. The materials for the formulations disclosed herein are mostly derived from the waste materials of the species of tree that nut is harvested from and/or from other natural sources.
