Low moisture foods such as grains, seeds, spices and flour are part of our daily diet. While they are rich in bioactive compounds, they can be minimally processed or often consumed raw. Several outbreaks due to Salmonella and E. coli O157:H7 have been attributed to low moisture foods. The efficacy of vacuum steam pasteurization in inactivation of Salmonella PT 30, E. coli O157:H7 and E. faecium on whole flaxseed, quinoa, sunflower kernels, milled flaxseed and whole black peppercorns was determined. The impact of pasteurization on microbial shelf life of whole and milled flaxseed was also monitored along with their water activity. Vacuum steam pasteurization was effective at inactivation of each bacteria, providing >5.0 log CFU/g reduction at temperatures as low as 75 and 85C. Also, there was no negative impact on microbial shelf life or water activity on pasteurized flaxseed as compared to unpasteurized products.