Purpose The nutritional richness of pigments derived from microalgae makes them a popular choice for food and food additives, serving as colorants in various food products. This study presents a new food prototype that combines phycocyanin-fortified cheese. Methods We conducted a comprehensive analysis of its physicochemical composition, colorimetric properties, antimicrobial and antioxidant capabilities, and textural and sensory evaluation over a period of 60-day and 15-day intervals. First, cyanobacterial sp. was cultured, the pigment was extracted, and analysis was performed. Then, the probiotic feta cheese with different concentrations of phycocyanin as control (without phycocyanin), 0.5%, 1%, and 1.5% phycocyanin powder were formulated, and various physiochemical, antioxidant, microbial, calorimetric, texture, and sensory analyses were performed. Results The results showed that feta cheese without phycocyanin had a higher value in tests of pH, moisture, syneresis, brightness index (L*), color change (Delta E), and microbial analysis, while the lowest value belonged to feta cheese with 1.5% of phycocyanin. In contrast, the tests of acidity, dry matter, protein, ash, antioxidant, water holding capacity, redness (a*), yellowness (b*), and texture properties, while the lowest measurements were observed in the control condition. The impact of phycocyanin on the lactobacillus population showed that increasing the concentration of pigment could have positive results. Additionally, PC enhanced the formulated cheese in terms of color, texture, consistency, and pleasantness, while the appearance, flavor, and odor decreased significantly. However, PC did not impact the salinity score. Conclusion In summary, pigments derived from Spirulina sp. have the potential to enhance the nutritional value and color of yogurt, making it a valuable organic effective component.