The microalga Chlorella and strains of Bifidobacterium have been used in human or animal food supplements for decades because of their positive health effects. The presented study assessed different properties of C. vulgaris and its combination with bifidobacteria with the aim to develop new functional foods. The growth of four bifidobacteria strains in milk and whey supplemented with 1.0% (w/v) C. vulgaris and the immunomodulatory effects of aqueous Chlorella solutions (0.5%, 1.0%, and 3.0%) on human peripheral mononuclear cells were evaluated. Furthermore, synergistic effects on lipid metabolism of rats fed a high-fat diet with Chlorella and B. animalis subsp. lactis BB-12^® were analysed. Chlorella had a positive growth-promoting effect on the tested bifidobacteria (p < 0.05), and significantly increased the secretion of inflammatory cytokines (tumor necrosis factor-α, interleukin-10, and interleukin-6), depending on the concentration of Chlorella (p < 0.05). After 8 weeks, significant synergistic effects of Chlorella and bifidobacteria on triglyceride levels in rat heart, liver, and serum were observed (p < 0.05). These results demonstrate that various combinations of Chlorella and bifidobacteria have significant potential for the development of new fermented products, dependent on the algal species, probiotic strain, application form, and concentrations for acceptable sensory quality for consumers.