Tree nuts such as pecans can be contaminated with pathogens including Salmonella enterica subspecies enterica during harvest, processing, and post-processing. Thus, a microbial reduction step such as heat treatment is recommended for pecan processors to produce a safe product. However, the quality of the final product may be affected by a thermal treatment. This research seeks to achieve a 5 log CFU/g reduction in a surrogate organism for Salmonella enterica: Enterococcus faecium on in-shell pecans using hot water or saturated steam. This research also studies the effects of these heat treatments on quality parameters of pecans including cracking efficiency, color, and moisture content. A 5 log CFU/g reduction in E. faecium was achieved using a hot water treatment at 90 °C for at least 3 min or saturated steam treatment at 100 °C for at least 4 min. No significant changes in moisture percentage or pecan testa color were found.