Lactobacillus plantarum was encapsulated by slowly digestible hydrolyzed heat-moisture-treated (hydrolyzed-HMT) black waxy rice and applied in yoghurt. Incorporating these microcapsules in yoghurt resulted in higher viability of Lactobacillus bulgaricus C49 and Streptococcus thermophilus C44, especially in prolonged storage. The viability of L. bulgaricus and S. thermophilus (7.98 and 8.28 Log CFU/g) in synbiotic yoghurt was higher than in the control (7.81 and 7.96 Log CFU/g). Thirty-two aromatic compounds were detected and classified into 4 groups: alcohols, carbonyls, organic acids, and sulfur. Synbiotic yoghurt produced higher carbonyl compounds, particularly acetaldehyde and diacetyl. On the other hand, higher organic acid especially hexanoic, dodecanoic, acetic, butanoic, and pentanoic acids was observed at the end of fermentation but did not differ from control after storage. Ethanol was also higher in the synbiotic yoghurt due to the breakdown of glucose from starch and acetaldehyde by lactic acid bacteria. Weak correlation was found concerning sulfur compounds. Rice starch granules were aggregated and still retained its hexagonal shape, indicating high resistance to acid fermentation during 28 days of storage. The resistant starch coating from rice could provide a good prebiotic ingredient and allow the design of synbiotic yoghurt with enhanced aroma.