The incorporation of lipid ingredients into food matrices presents a main drawback—their susceptibility to oxidation—which is associated with the loss of nutritional properties and the generation of undesirable flavors and odors. Oil-in-water emulsions are able to stabilize and protect lipid compounds from oxidation. Driven by consumers’ demand, the search for natural emulsifiers, such as proteins, is gaining much interest in food industries. This paper evaluates the in vitro emulsifying properties of protein hydrolysates from animal (whey protein concentrate) and vegetal origin (a soy protein isolate). By means of statistical modelling and bi-objective optimization, the experimental variables, namely, the protein source, enzyme (i.e., subtilisin, trypsin), degree of hydrolysis (2–14%) and emulsion pH (2–8), were optimized to obtain their maximal in vitro emulsifying properties. This procedure concluded that the emulsion prepared from the soy protein hydrolysate (degree of hydrolysis (DH) 6.5%, trypsin) at pH 8 presented an optimal combination of emulsifying properties (i.e., the emulsifying activity index and emulsifying stability index). For validation purposes, a fish oil-in-water emulsion was prepared under optimal conditions, evaluating its physical and oxidative stability for ten days of storage. This study confirmed that the use of soy protein hydrolysate as an emulsifier stabilized the droplet size distribution and retarded lipid oxidation within the storage period, compared to the use of a non-hydrolyzed soy protein isolate.