Whey protein hydrolysates with enhanced bioactivities may confer improved health benefits to the consumers. While some studies have shown the protein ingredients produced through conjugation with maltodextrin to have greater functionality, the effect of conjugation on the bioactivities is not clearly established. In this study, whey protein concentrate WPC80, isolate WPI90, and hydrolysates WPH10, WPH15 and WPH20 were screened for bioactivities (antimicrobial activity by agar well assay, antioxidant activity by ABTS⁺ radical assay and antihypertensive activity by ACE inhibition assay). Hydrolysate WPH10, exhibiting the highest bioactivities was conjugated with maltodextrin to obtain a thermally stable conjugated solution. A batch of 2L conjugated solution was spray dried in a Niro drier with an inlet and outlet temperature of 200°C and 90 ± 5°C, and alternatively, freeze-dried at −80°C under 50 mTorr vacuum. The bioactivities of the conjugated samples were then assessed according to the above-mentioned assays. All experiments were conducted in triplicates and one-way ANOVA was applied to differentiate the mean values. The hydrolysates showed significantly (P < 0.05) higher bioactivities (10.6 ± 0.33mm, 766.72 ± 13.3 TEAC µmol/L and 67.52 ± 0.2% for antimicrobial, antioxidant and antihypertensive activity), as compared with concentrate (8.6 ± 0.33mm, 373.3 ± 21.5 TEAC µmol/L and 60.8 ± 0.1%) and isolate (9.3 ± 0.33mm, 426.9 ± 42.0 TEAC µmol/L and 62.9 ± 0.07%). Based on the highest bioactivity, hydrolysate WPH10 was selected for conjugation with maltodextrin. The conjugated WPH10 solution demonstrated higher antimicrobial (17.16 ± 0.33mm) and antioxidant activity (1044.37 ± 39.1 TEAC µmol/L) (P < 0.05), whereas a slight decrease in the antihypertensive activity (65.4 ± 0.2%) was observed, as compared with WPH10 alone. Subsequent spray and freeze drying of the conjugate solution exhibited even higher antimicrobial (18.5 ± 0.57mm) and antioxidant activity (1268.89 ± 41.9 TEAC µmol/L) (P < 0.05), while retaining the antihypertensive activity (65.6 ± 0.3%) i.e., (P > 0.05). Further studies are in progress to develop health formulations utilizing WPH-conjugates with enhanced bioactivity and functionality.