Pistachio (Pistacia vera L.) is one of Iran’s most valuable export commodities, and maintaining its hygienic quality is essential to compete in global markets. Microbial contamination and mycotoxins (particularly aflatoxin) are the primary causes of export shipment rejections and damage to the product’s reputation. Traditional disinfection methods, such as sodium hypochlorite, face limitations due to the formation of harmful by-products and reduced efficacy in the presence of organic matter. In recent years, peracetic acid has gained attention as a potent, safe, and environmentally friendly oxidant that decomposes into harmless residues (water, oxygen, and carbon dioxide). This review aims to comprehensively analyze the mechanism of action, efficacy, challenges, and prospects of peracetic acid application in pistachio processing. Findings demonstrate that a 1% peracetic acid solution in terminal washing tanks can reduce microbial load (bacteria and fungi) by up to approximately 100% without negatively affecting lipid percentage, peroxide value, or sensory properties. The primary antimicrobial mechanism involves oxidation of proteins, membrane lipids, and DNA of microorganisms. The absence of chemical residues and cost-effective operation are key advantages of this approach; however, challenges such as the gradual decline in effective concentration in the presence of organic matter necessitate continuous monitoring and process optimization. Overall, peracetic acid is proposed as an effective, safe, and sustainable agriculture-compliant disinfectant and a strategic alternative to chlorinated compounds in Iran’s pistachio industry.