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The growing demand for high-quality gluten-free bread requires innovative technological and functional approaches. This study investigates, for the first time, the use of Lacticaseibacillus paracasei SP5, in free and immobilized form on traditional Greek trahanas, for producing GF sourdough bread based on rice and buckwheat flour. Sourdough breads produced with free and immobilized cells displayed greater performance than the control sourdough bread in microbial stability and physicochemical properties, with the immobilized form showing the best results. In particular the application of immobilized L. paracasei SP5 led to gluten free sourdough bread with enhanced acidification (pH 4.55; TTA 12.9 mL) and remarkable lactic (2.20 g/kg) and acetic acid (0.76 g/kg) levels, extending the shelf-life to 7.0 days against mold and 7.5 days against rope spoilage, statistically significantly higher than the other two gluten free sourdough samples. It also showed the strongest antifungal activity and improved technological characteristics, including higher loaf volume (2.84 mL/g), greater height (5.50 cm), and lower baking loss (17.42%). Total phenolic content (87.3 mg GAE/100 g) and antioxidant capacity were also statistically significantly increased. Overall, immobilized L. paracasei SP5 on trahanas appears to be a promising clean-label strategy to improve quality, shelf-life, and functional value of GF bread.