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Designing stable dried functional food ingredients and foods containing live probiotic cultures maintaining high viable cell loads at the time of consumption is a challenge for the industry. The aim of the present study was the development of stable freeze-dried functional food ingredients with enhanced shelf-life during long storage. Zea flakes, pistachios, and raisins were used as immobilization supports for the wild-type presumptive probiotic strains <i>Pediococcus acidilactici</i> SK and <i>Lactiplantibacillus plantarum</i> F4, while <i>L. plantarum</i> B282 was used as a reference strain. Cell survival was monitored during storage at room and refrigerated temperatures for up to 6 months. Levels of freeze-dried cultures were maintained up to 7.2 logcfu/g after 6 months storage at room temperature and up to 8.5 logcfu/g at refrigerator temperature, in contrast to free cell levels that ranged <7 logcfu/mL, suggesting the positive effects of immobilization and freeze-drying on cell viability. Of note, levels of freeze-dried immobilized <i>P</i>. <i>acidilactici</i> SK cells on zea flakes and pistachios remained stable after 6 months of storage at 4 °C, ranging 8.1–8.5 logcfu/g (survival rates 98.2 and 99.7%, respectively). The technology developed presents important advantages for the maintenance of cell viability during storage, assuring stability of ready-to-use functional food ingredients that could be directly incorporated in food systems.