Soy sauce, a widely consumed condiment, undergoes intricate physicochemical transformations during its natural fermentation process. This research delved into the analysis of physical and chemical properties in naturally brewed soy sauce, aiming to elucidate the impact of fermentation stages (Koii, earlier moromi, final moromi, soy sauce product) and sample variations on these properties. Parameters such as pH, total acid, total soluble solids, and water activity (aw) were assessed. Additionally, chemical attributes were analyzed, including total nitrogen, crude protein, formol nitrogen, and sodium chloride (NaCl) content. The correlation between physical and chemical properties during the fermentation stages was determined using the principal component analysis (PCA) method. The fermentation process significantly affected soy sauce's physical and chemical properties. Key factors include total dissolved solids, water activity, total acids, salt, total nitrogen, crude protein, and formol nitrogen, which display distinct patterns. These fluctuations were primarily driven by microbial activity and enzymatic hydrolysis, and total nitrogen, crude protein, and formol nitrogen play pivotal roles in characterizing soy sauce quality. Remarkably, total acid content and pH values exhibited significant variations that deviate from expected correlations due to weak acids. Samples C and D were deemed the most suitable out of the five tested, aligning better with quality standards for soy sauce. This study sheds light on the complex physicochemical changes during soy sauce fermentation, emphasizing the impact of raw materials and microbial processes on its properties.