Kombucha is a fermented tea known for its health benefits, including antimicrobial properties and immune-boosting effects. However, improper home brewing practices can lead to contamination by harmful bacteria, raising concerns about food safety and health. This study evaluated the survival levels of Salmonella and its interactions with microbial dynamics and assessed changes in the natural microbial environment during fermentation. It also investigated the physicochemical properties and changes in indigenous microbial analysis during fermentation. The kombucha was prepared using black tea and SCOBY cultures under controlled conditions at 25 °C for 14 days (0, 1, 2, 3, 5, 7, 10, and 14 days). Microbial and physicochemical analyses were conducted at various time points over 14 days, measuring pH, acidity, antioxidant activity, organic acids, and polyphenols. Microbial analyses (aerobic plate counts, lactic acid bacteria LAB, total yeast and mold, and Salmonella enumerations) were performed in triplicate, using Petrifilm, MRS, PDA and XLT4 media, respectively. Genomic analysis of the SCOBY (pre- and post-fermentation) via 16S rRNA sequencing was used to characterize microbial changes and assess their inhibitory effects on Salmonella. The significance (p ≤ 0.05) of differences between mean values was determined using a two-way analysis of variance (ANOVA). The initial Salmonella population of 7.30 log CFU/mL significantly (p ≤ 0.05) decreased to below detectable limits (<1 log CFU/mL) by day 10 in the kombucha. The LAB also increased from 4.95 to 6.91 log CFU/mL within 10 days; the reductions in Salmonella and the increase in LAB, respectively, correlate with decreases in pH and increases in organic acid concentrations. Total yeast and mold and APC recorded increased (4.2 to 5.95 log CFU/mL) and (4 log CFU/mL) respectively over the 14 days. After fermentation, total polyphenols and antioxidant activity increased, which may be a potential indication of antimicrobial effects. Meanwhile, the sugar content decreased, indicating active fermentation. This study illustrated the microbiological safety of home-brewed kombucha, identifying critical factors that influence pathogen survival.