Encapsulation techniques are generally used to preserve the volatile compounds of essential oils. This study aimed to evaluate the influence of process variables on the microencapsulation of marjoram essential oil (MEO) (Origanum majorana L.) by ionic gelation. The effect of sodium alginate concentration (0.5–2 g/100 mL), emulsifier concentration (0.5–2 g/100 mL whey protein isolate (WPI)), and cationic bath concentration (0.05–0.3 mol/L CaCl2) on the emulsions and beads properties were investigated, according to a rotatable central composite design. MEO chemical composition and antimicrobial activity were assessed. Emulsions were characterized for droplet size and viscosity, while the particles were analyzed for encapsulation efficiency, size and circularity, and morphology. High concentrations of alginate and WPI intensified the porous structure of the beads, reducing droplet mean diameter and encapsulation efficiency. High alginate concentrations also increased emulsion viscosity, affecting positively beads' circularity. The intermediate concentration of sodium alginate (1.25 g/100 mL), WPI (1.25 g/100 mL), and CaCl2 (0.175 mol/L) were selected as the most appropriate conditions to produce beads with satisfactory circularity and high encapsulation efficiency.