The demand for functional foods is increasing, particularly concerning plant-based probiotic products. These products are becoming a popular alternative to dairy-based options. However, fermented vegetables have a high salt content, which can have negative effects on health if consumed excessively. There has been difficulty in finding the right balance in terms of the salt concentration for the high-quality fermentation of vegetables. To preserve its valuable nutrients and ensure maximum quality, as a vegetable, yellow beetroot was used. The aim of this study was to increase the lactic acid bacteria and preserve the active compounds in fermented yellow beetroot. The research used varying salt levels in brine (0–6%) to examine their impact on the physical, chemical, and microbiological properties, as well as the degradation temperatures and thermal analysis. Moreover, to create a new product, fermented beetroot was freeze-dried. This study found that stable products were obtained after 4 and 8 days due to the development of lactic acid bacteria. The addition of salt did not affect the stability of the products, but it did affect the active ingredients. Higher salt additions resulted in more salt penetrating into the beetroot tissue, impacting the amount of salt consumed. Our study found that a 1% addition of salt led to higher levels of active ingredients and satisfactory amounts of bacteria. Yellow beetroot, with its high content of polyphenols, pigments and lactic acid bacteria, can be used as a healthy ingredient in a diet after undergoing a freeze-drying process. These research findings provide valuable insights into optimizing the salt content to preserve the lactic acid bacteria, nutrients, and desirable color characteristics of fermented yellow beetroot.