In vitro activity of nine cyanobacterial and ten microalgal newly isolated or culture collection strains against eight significant food-borne pathogens has been evaluated and compared. Water extracts and culture liquids of Gloeocapsa sp. and Synechocystis sp. demonstrated the widest spectrum of activity with minimal inhibitory concentration (MIC) ranging from 1.56 to 12.5 mg mL−1. Culture liquid of Anabaena sp. had the highest activity (MIC = 0.39 mg mL−1) but only to Gram-positive bacteria. Ethanol extracts and fatty acids from all cyanobacteria and microalgae were active against Streptococcus pyogenes and/or Staphylococcus aureus. The fatty acids of Synechocystis sp. inhibited the growth of Bacillus cereus, Escherichia coli and Candida albicans (MIC values of 2.5–1.25 mg mL−1, respectively). Exopolysaccharides (EPS) of Gloeocapsa sp. were the sample that exhibited activity against all test pathogens with lowest MIC values (0.125–1 mg mL−1). High activity with a narrower range of susceptible targets demonstrated the exopolysaccharides of Synechocystis sp. and Rhodella reticulata. Antimicrobial activity was proven for phycobiliproteins isolated from Synechocystis sp., Arthrospira fusiformis, Porphyridium aerugineum and Porphyridium cruentum, respectively. In conclusion Gloeocapsa sp. and Synechocystis sp. and especially their exopolysaccharides showed the most promising potential against the examined food pathogens.