This study determined the effects of physicochemical and microbial properties of emulsion as a fat replacer in meat analogs during freezing storage. Meat analogs were prepared with different fat replacers: vegetable oil (O) for control, oil in water emulsion (E), and non-emulsified oil in water emulsion (EC) for emulsion control. After that, meat analogs were stored for 0.5, one, three, and six months at −18 °C and −60 °C. The results showed that the drip loss of all samples was not significantly different (p > 0.05). However, the liquid holding capacity of EC and E was significantly higher than that of O (p < 0.05). Additionally, the microstructures of meat analogs of E and EC were smaller with denser pore sizes than O. This explains the significantly lower hardness of E and EC compared to O (p < 0.05). Overall, E showed superior physiochemical and sensory quality. During the storage, the stability of chemical properties, such as volatile basic nitrogen and thiobarbituric acid reactive substances, showed no significant changes (p > 0.05). Moreover, the microbial studies (total viable counts and Escherichia coli count) suggested that meat analogs did not deteriorate during the preparation and storage. Thus, this study suggests that emulsion-type fat replacers influence meat analogs’ physicochemical and sensorial properties. However, these properties are not influenced by the storage temperature and duration.