With the increased consumer demand for nutritional foods, it is important to develop novel products with enhanced health benefits and functionality. We developed a spray dried health formulation by encapsulating probiotics in a conjugated whey protein matrix. Samples of whey protein concentrate, isolate and hydrolysates were screened for bioactivities (antimicrobial, antioxidant and antihypertensive activity) and based on highest bioactivities hydrolysate WPH10, was conjugated with maltodextrin to obtain a thermally stable conjugated solution. Probiotic cultures Bifidobacterium animalis ssp. lactis ATCC27536 and Lactobacillus acidophilus ATCC4356 were added in the conjugated solution at ratio of 1:1, with spiking level of log₁₀ cfu/mL. The mixture was spray dried in 2-L batch using a Niro drier with an inlet and outlet temperature of 200°C and 90 ± 5°C. To conduct the storage stability, the dried formulation was stored in airtight bottles for 10 weeks at 4, 25, and −18°C, to monitor cell viability, moisture and functionality. The experiments were done in triplicates and one-way ANOVA was applied to differentiate the mean values. In comparison to WPH10 alone, the conjugated WPH10 solution demonstrated higher antimicrobial and antioxidant activities. Following spray drying a higher antimicrobial (18.5 ± 0.57 mm) and antioxidant activity (1268.89 ± 41.9 TEAC µmol/L) was observed with retention in the antihypertensive activity (65.6 ± 0.3%ACE inhibition). The mean probiotic counts in conjugated WPH10 matrix before and after spray drying were 10.37 log cfu/mL and 8.50 log cfu/g, respectively. These counts were maintained for at least 4 weeks under all 3 storage conditions. Beyond that, the viability gradually decreased and at 10 weeks of storage the counts were 3.79 and 4.03 cfu/g at 4 and −18°C, respectively. At this point, the moisture content was 0.94 ± 0.14%, with a slight increase in the wetting time (from 47 ± 2min to 61 ± 3min) and decrease in the solubility (from 90.7 ± 0.13% to 82.2 ± 0.4%). Such formulation can be applied in functional foods to harness their enhanced health benefits and functionality.