Almonds are one of the highest valued crops in the United States, resulting in an industry that produces more than 2 billion pounds of kernels annually. With an increasing yearly production, it is critical to understand the effects of weather and processing on almond quality and determine chemical safety. This research addresses three aims: determine the effect of postharvest moisture (i.e. rain) exposure during storage on raw and roasted almonds, elucidate the effect of pasteurization on raw almond quality during shelf life, and establish glutathione as an endogenous nucleophile involved in acrylamide scavenging during storage. The first aim of this work determined that postharvest moisture exposure followed by pre-processing drying shortens almond shelf life up to 50%. Shelf life is especially compromised in almonds roasted at high temperatures to achieve darker color roasts. This established that almonds exposed to moisture and/or high humidity after harvest should be prioritized in processing and avoid high temperature processing. The second aim addresses the effect of chemical (propylene oxide) and moist heat pasteurization on lipid oxidation in raw almond during storage. Chemical and sensorial analyses demonstrated that moist heat pasteurization protected raw almonds from lipid oxidation with significantly lower rancidity-associated volatiles and negative sensory attributes starting at 4 months of storage, which suggests longer shelf life. The third aim of this work determined scavenging mechanisms to explain acrylamide (a naturally occurring probable carcinogen) losses in almond products during storage. We observed significant decreases in acrylamide levels (21.8 %) over 12 weeks of storage. Acrylamide undergoes Michael addition reactions with nucleophiles including some amino acids and glutathione. Free amino acids and glutathione concentration were measured for the first time in California almonds before and after roasting. An acrylamide-glutathione conjugate was identified in roasted almonds. This product increases during storage demonstrating that endogenous nucleophiles are involved in acrylamide scavenging during storage. Overall, this work provides the nut industry with information on how to better manage the crop to reduce food waste in response to climate change. Additionally, these studies support the use of steam pasteurization of almonds for ensuring food safety and promoting extended shelf life for food security. The improved understanding of the acrylamide rate of decline and the reaction between acrylamide and free amino acids and glutathione encourages future improvement in chemical food safety.