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The aim of this study was to microencapsulate probiotic bacteria (<i>Lactobacillus acidophilus</i> 11073) using whey-protein-isolate (WPI)–octenyl-succinic-anhydride-starch (OSA-starch)-complex coacervates and to investigate the effects on probiotic bacterial viability during spray drying, simulated gastrointestinal digestion, thermal treatment and long-term storage. The optimum mixing ratio and pH for the preparation of WPI-OSA-starch-complex coacervates were determined to be 2:1 and 4.0, respectively. The combination of WPI and OSA starch under these conditions produced microcapsules with smoother surfaces and more compact structures than WPI-OSA starch alone, due to the electrostatic attraction between WPI and OSA starch. As a result, WPI-OSA-starch microcapsules showed significantly (<i>p</i> < 0.05) higher viability (95.94 ± 1.64%) after spray drying and significantly (<i>p</i> < 0.05) better protection during simulated gastrointestinal digestion, heating (65 °C/30 min and 75 °C/10 min) and storage (4/25 °C for 12 weeks) than WPI-OSA-starch microcapsules. These results demonstrated that WPI-OSA-starch-complex coacervates have excellent potential as a novel wall material for probiotic microencapsulation.