The key volatiles of fermented noni juice (FNJ) were identified, and the effect of microencapsulation (via spray drying and freeze drying) on the volatile profile of FNJ powders was investigated. Results showed that hexanoic acid was the major contributor to the unpleasant odour of FNJ. Both drying methods significantly reduced (p < 0.05) the retention of volatiles, and changed the volatile profile of the resulting powders. Comparing the two methods, volatile retention in the spray-dried powder was lower, and was negatively affected by the increase of drying air temperature (p < 0.05). The odour activity values (OAVs) of key volatiles decreased after microencapsulation, however, most of them were still present, and contributed to the overall odour of the powders. This research has provided qualitative and quantitative data on the volatiles of FNJ, and explored for the first time, the influence of microencapsulation on the volatile characteristics and retention in powders.