Palm is believed the oldest domesticated plant over the history of human and has been utilized for versatile products. Palm wine is one of the products that have recognised for traditions and cultures in tropical and subtropical countries. Palm wine is made of naturally fermented palm sap, which is significantly influenced by ecological factors and genomic characteristics of its microbial communities. We assessed microbial and metabolite characteristics of palm wine to understand the fermentation nature, covering the influence of seasonal sap tapping and palm species. We found a swift fermentation process through the depletion of sugar within a few days, indicating a short shelf life of palm wine. Mixed acidic fermentation accompanied by the growth of lactic acid and acetic acid bacteria occurred at the same time as ethanol production, driven by a co-working of Saccharomyces cerevisiae and Zymomonas mobilis. S. cerevisiae was more assertive to the change of micro-ecological factors in the fermentation process and its genomics properties likely indicate to local geographic adaptation possessing slower evolutionary trajectory as they are still exposed to naturally occurring microbial communities. Seasonal sap tapping likely unchanged the core microbial species and metabolite composition, but they may contribute to specialize product signature. Profile of volatile esters, such as ethyl 9-decenoate, octanoic acid, and decanoic acid have set a baseline on determining the fermentation stage characters, capturing every palm species. By understanding the nature of palm wine fermentation, we can elaborate a better perspective to manage microflora for aroma and flavour, to achieve intended quality and product stability, to establish further product development, and more importantly to appreciate this traditional beverage.