Achieving both the maintenance of the highest live microbial population possible, while limiting the production of ethanol and overpressure in kombucha bottles, constitutes a challenge that requires gaining insights into the shelf life of kombucha. This field study aimed at understanding the impact of biotic and abiotic factors (microbial activity and storage temperature respectively) on bottled unflavored and flavored kombuchas during their shelf life. Changes in the microbial and chemical compositions were monitored over 1 to 8 months of storage at 4 °C or 20 °C. Non-targeted analysis of volatile compounds was carried out to identify biomarkers across chemical families and put into perspective with a descriptive sensory analysis. Results show the efficiency of refrigeration and pasteurization to inhibit alcoholic fermentation. However, flavoring strongly accelerated yeast fermentative activity despite refrigeration leading to excessive ethanol concentrations and in-bottle pressures. This may be caused by the introduction of assimilable nitrogen through flavoring ingredients. Fatty acids were determined as biomarkers for aging during cold storage with or without flavoring. Despite changes in volatile composition, olfactory sensory profiles were mildly impacted. Ammonium supplementation stimulated microbial activities before bottling (aerobic phase) but not after, hinting at an effect of amino acids during the shelf life. This study advises kombucha producers to pay greater attention to the assimilable nitrogen content of flavoring ingredients to improve the control over the quality of their final products during the shelf life.