Cell free extracts (CFE) obtained from Lactobacillus plantarum FI 8595 and Lactobacillus reuteri ATCC 55730 alone or in combination with propolis ethanolic or water extracts (1%) were microencapsulated with maltodextrin (25%) before the subsequent spray drying process. They were morphologically characterized by scanning electron microscope. Chemical compositions of pure extracts were identified by gas chromatography–mass spectrometry. Antimicrobial activities of pure and microencapsulated extracts against four foodborne pathogens (Staphylococcus aureus ATCC29213, Listeria monocytogenes ATCC19112, Klebsiella pneumoniae ATCC700603 and Salmonella Paratyphi A NCTC13) were determined using agar well diffusion, broth microdilution and time kill assays. CFE from L. reuteri and L. plantarum consisted of acetic acid, pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(phenylmethyl)-, 2,3,4-trihydroxybenzaldehyde and 9-octadecenoic acid. The results also indicated the presence of two respective major compounds, namely, 2-methoxy-4-vinylphenol (19.03%) and trans-cinnamic acid (27.67%) in water and ethanolic propolis extracts. Presence of propolis extracts mainly ethanolic extract in microencapsulation led to higher inhibition zones against all foodborne pathogens (p < .05). The co-microencapsulation of CFE from L. reuteri in combination with ethanolic or water extract of propolis resulted in 2.34- and 2.2-fold higher inhibition zone towards L. monocytogenes. Pure and microencapsulated CFE from L. reuteri resulted in 2.89 and 2.14 log cfu/ml reduction in growth of S. Paratyphi A at 3 hr, respectively. The co-microencapsulation of CFE from lactobacilli and propolis extracts mainly ethanolic extract could be suggested as a novel antimicrobial on inhibition of food pathogens, as they contain abundant bioactive substances.