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The aim of this study was to compare the ability of endogenous Lactobacillus paracasei ATR6 to grow in unsupplemented bovine cheese whey (CW) and ricotta whey (RW), and to evaluate the efficiency of these media as encapsulating agents for the spray-drying (SD) of this bacterium. Growth assays indicated that both CW and RW are adequate culture media since L. paracasei ATR6 grew satisfactorily (~ 4 log cycles) in both compared to the control medium (skimmed milk). Concerning their potential as encapsulating agents, results showed that survival rates after SD were similar for CW and RW (> 78%), as were the yields (> 47%) of this process. CW allowed the formation of smaller capsules (5.31 ± 1.27 μm) than RW (15.21 ± 7.24 μm), with lower moisture: 8.60% and 13.52%, respectively. Powders were stored at 25 °C for 60 days, during which CW and RW maintained satisfactory bacterial viability. Water activity increased, yet remained below 0.3. Moisture content of CW and RW powders was relatively stable throughout the 60 days; however, values obtained in this study are considered to lie outside the adequate range (4–7%) for product stability. We did not observe color changes in CW and RW microcapsules during storage. Due to its lower protein content, RW offered less protection, which led to higher loss in acidification ability of the strain. CW and RW are suitable culture media and encapsulating agents for the growth of L. paracasei ATR6; however, the former offered better protection, which enabled the maintenance of biological activity. [ABSTRACT FROM AUTHOR]