Fortified dairy products such as yogurt have attracted a lot of attention due to the increasing concern for public health. This study aimed to determine the effects of nanoemulsified and a microencapsulated protein hydrolysate obtained from Planiliza abu on some of the properties of yogurt. The physicochemical, rheological, microbiological, and sensory evaluation of the fortified yogurt samples stored at 4°C were assessed during 21 days. The fish protein hydrolysates (FPHs) < or >10 kDa protein were used. The amino acid profile of Planiliza abu was glutamic acid (78.99%), aspartic acid (59.53%), and lysine (53.54%). No significant change was observed in titratable acidity (TA) and pH of supplemented yogurts during refrigeration. The highest survival level of lactic acid bacteria (LAB), water‐holding capacity (WHC), and viscosity and the lowest syneresis were observed in fortified samples with FPH <10 kDa. The highest ferric reducing antioxidant power (FRAP) was achieved in yogurt fortified with nanoemulsion FPH < 10 kDa (NEh10a, 0.41 mg/g). The results showed that fortified yogurt with FPH, particularly less than 10 kDa, is among the desirable functional food with appropriate gel network and consistency as well as better taste and mouth feel, and higher overall acceptance.