Okara (soybean residue) is a food processing by-product and is often under-utilised due to its low digestibility and off-odour. To improve its composition, a combination of different biocatalysts was used. Okara was first treated with a carbohydrase Viscozyme® L, then fermented with probiotic Lactobacillus paracasei and/or yeast Lindnera saturnus. Viscozyme® L reduced the amount of insoluble fibre by 41.5% and increased soluble fibre by 117%. L. saturnus significantly increased the amount of esters in okara, leading to a perceptible fruity aroma. The final cocultured okara contained high cell counts of live probiotics, significantly less insoluble fibre, soluble fibre, and greater amounts of free amino acids, isoflavone aglycones and fruity esters. After 6 weeks, probiotic viability did not significantly change when stored at 5 °C, but decreased by 1.35 log colony-forming unit/mL when stored at 25 °C. Nonetheless, the amount of viable probiotic cells exceeded the minimum dosage for conferring health benefits. With enhanced nutritional and aroma profiles, the cocultured okara may be a functional probiotic beverage.