On the whole, this research investigates the practical implementation of two Kyrgyz companies—Semeynye Traditsii (ice cream maker) and Ak-Alman LLC (fish product manufacturer)—whose ISO 22000 and HACCP food safety management systems were observed in use. The topic was selected since, in emerging nations, worldwide food safety recommendations for small and medium-sized businesses (SMEs) become even more important. Both companies are under greater and more pressure to follow world standards as export and market credibility depend on it. Evaluating operational impact, understanding motivations, assessing certification readiness, and comparing challenges between the two businesses were the key objectives of the study. The study took a qualitative approach depending on in-depth interviews conducted between late 2024 and spring 2025. The two case study companies were selected according to varying degrees of ISO implementation. Semeynye Traditsii was in early planning whereas Ak-Alman LLC had completed internal audits and set ISO-compliant policies previously. Data was gathered via semi-structured interviews; they were then thematically evaluated and interpreted in view of ISO standards, internal control points, manufacturing quality, and strategic planning. Important findings revealed that Ak-Alman gained much from fast adoption supported by an experienced outside consultant. Among the quantifiable improvements the business accomplished were a 20–25% expansion in customer base and longer product shelf life. Semeynye Traditsii stressed laboratory modernization, improved traceability, and future certification as means of export expansion, though less developed in application. Neither company considered ISO as a formality; rather, it was a calculated investment. The main outcome of the comparison is that progressive integration of food safety culture, professional support, and leadership commitment define most of the achievement of ISO certification. The main advise is that Kyrgyz SMEs should consider artificial implementation strategies supported by continuous training and, if at all possible, access to certified outside consultants.