Microencapsulation of hydrophobic (α-tocopherol) and hydrophilic (ascorbic acid) vitamins by native (non-modified) and modified soy protein isolate (SPI) was carried out using a spray-drying technique. Proteins' functional properties were modified by acylation and cationization reactions in aqueous alkaline media. The results obtained demonstrated that SPI modification resulted in decreased emulsion droplet size and viscosity. All preparations with ascorbic acid (AA) had lower viscosity and microparticle size than those with α-tocopherol (T). Moreover, grafting of fatty acid chains to SPI by acylation improved its amphiphilic character and affinity with hydrophobic substances. Thus, the microencapsulation efficiency of T was increased from 79.7% to 94.8% and the microencapsulation efficiency of AA was reduced from 91.8% to 57.3% compared to native SPI. Conversely, attachment of quaternary ammonium cationic groups to proteinic chains by cationization, increased SPI solubility and favored the AA microencapsulation. This study illustrated that an appropriate modification of SPI can improve the microencapsulation efficiency of suitable active cores. Display omitted •Soy protein isolate (SPI) is an efficient wall material for microencapsulation.•SPI acylation results in enhanced retention efficiency (RE) of hydrophobic core.•SPI cationization improves the microencapsulation of hydrophilic core.•Affinity between core and wall materials plays a major role in encapsulation.•Appropriate modification of SPI can improve RE of suitable active cores.