Co-microencapsulations of cell-free extract (CFE) obtained from Lactobacillus reuteri with propolis water and ethanolic extracts (1% of CFE) were made to investigate their enhanced antibacterial activities against four fish spoilage bacteria (Pseudomonas luteola, Enterobacter cloacae, Photobacterium damselae, and Proteus mirabilis). Minimum bactericidal (MBC) and minimum inhibitory (MIC) concentrations of the pure and microencapsulated samples were identified by the broth microdilution method, while agar well diffusion method was used to find inhibition diameter zone of extracts. Chemical content of microencapsulated samples was also detected by gas chromatography-mass spectrometer (GC–MS). GC–MS analysis results showed that microencapsulated CFE from L. reuteri in combination with propolis extracts (aqueous and ethanolic) contained organic acids, hydrocarbons, phenolic acids/flavonoids, and benzene derivatives. P. mirabilis was the most sensitive fish spoilage bacteria against CFE from L. reuteri. Bacteriostatic effect of CFE from L. reuteri against P. mirabilis and P. luteola was enhanced by microencapsulation process. The combination form of microencapsulated CFE from L. reuteri with aqueous propolis extract showed a MIC of 25 mg/mL on the growth of P. mirabilis. Microencapsulated CFE from L. reuteri combined with ethanolic propolis extract completely killed P. damselae and P. luteola at a level of 50 mg/mL. The study results revealed that the combined use of propolis extracts, especially ethanolic extract with CFE obtained from L. reuteri in microencapsulation, generally showed a higher antimicrobial effect on all tested bacteria.