<p>Sausage is a widely consumed meat product that provides a favorable environment for the growth of foodborne pathogens due to its nutrient composition. This study aimed to produce a probiotic sausage enriched with 1% (w/w, based on total batter weight) phycoerythrin nanoemulsion and evaluate its effect on the viability of <i>Bacillus coagulans</i> microencapsulated with exopolysaccharides from <i>Aliinostoc</i> sp. 2. The cyanobacterial strain was cultured, and its exopolysaccharides and phycoerythrin pigment were extracted and purified to prepare the nanoemulsion. <i>B. coagulans</i> was microencapsulated, and the minimum inhibitory concentration (MIC) of the nanoemulsion was determined. Sausages were subjected to four treatments: control, 1% phycoerythrin nanoemulsion, <i>B. coagulans</i> (10⁷ cfu/g), and 1% phycoerythrin nanoemulsion + <i>B. coagulans</i> (10⁷ cfu/g). Physicochemical (pH, water activity, moisture, protein), microbial, color, lipid oxidation (TBA, peroxide value), antioxidant (DPPH, ABTS), and sensory analyses were performed on raw and cooked samples. Moisture content in cooked sausages was highest in the 1% nanoemulsion + <i>B. coagulans</i> treatment and lowest in the control, while protein content remained similar across treatments. Probiotic survival at the end of storage increased by approximately 18–22% in sausages with nanoemulsion + <i>B. coagulans</i> compared to <i>B. coagulans</i> alone. Total microbial counts (non-lactic bacteria), mold/yeast, psychrotrophic aerobic bacteria, and <i>Staphylococcus aureus</i> were significantly reduced in the combined treatment, and all samples remained free of coliforms, <i>E. coli</i>, and <i>Salmonella</i>. Color stability (L*, a*, ΔE) was better maintained in the nanoemulsion + <i>B. coagulans</i> treatment, while TBA and peroxide values indicated slower lipid oxidation. Antioxidant activity measured by DPPH and ABTS assays was highest in this treatment. Sensory scores for aroma, flavor, color, texture, and overall acceptability declined over 30 days in all samples but remained significantly higher in sausages with <i>B. coagulans</i> and nanoemulsion. Incorporation of 1% phycoerythrin nanoemulsion based on total batter weight, together with microencapsulated <i>B. coagulans</i>, enhanced probiotic viability, antioxidant capacity, color stability, and sensory quality, without making absolute claims regarding safety. These findings suggest a promising approach for developing functional meat products with improved shelf-life, nutritional quality, and consumer acceptability.</p>