The prevalence of functional foods has increased within the industrial production era. In this context, microalgae (including cyanobacteria) have become an innovative and promising resource of nutritional supplements as they are commercially cultivated to produce valuable compounds, including protein, pigments, lipids, essential amino acids, monounsaturated and polyunsaturated fatty acids, carotenoids, steroids, and vitamins, among others. Specifically, Arthrospira (Spirulina) platensis, which has been recognized as safe (GRAS) for human consumption, provides important properties, such as anticancer and antihypertensive activity, immune system enhancement, high content of antioxidants, vitamins and trace elements, and it belongs to the category of superfoods. Concerning the above, the main target of the current study was to produce a novel functional feta-type cheese with incorporated Spirulina and study its effect on microflora and physicochemical properties of produced cheeses. Feta cheese was prepared with pasteurized sheep milk. The effects of supplemented Spirulina (0.25%) were studied during manufacture and storage (4 °C) of feta-type cheese for 60 days and compared with commercial feta cheese. Growth and viability of Lactobacilli and Lactococci were reported more often in cheese samples containing Spirulina and, as a result, the starter culture (lactic acid bacterial culture) used in feta cheese production is not disturbed, and can be even enhanced, by the presence of microalgae. Specifically, Spirulina showed a positive effect on the growth of Lactobacilli, while Lactococci viability was detected enhanced in cheese sample with incorporated Spirulina. In addition, no pathogenic microorganisms were detected after the 30th day of production. Finally, incorporation of Spirulina significantly affected the color and mouthfeel of produced cheeses, while higher moisture content was detected as the content of Spirulina increased. To conclude, Spirulina has great industrialization potential as an additive in dairy products, and especially ones produced by Lactobacilli as starter cultures, while enhancing products nutritional value in parallel.