Filled hydrogel particles can be used to encapsulate, protect, and deliver lipophilic components. In this study, we investigated the influence of preparation conditions on the size of filled hydrogel particles created using biopolymer phase separation and enzymatic cross-linking. We then investigated the stability of these particles to external stresses: pH (pH 2-8); heat (40°-90°C, 20 min); sodium chloride (0-500 mM); and calcium chloride (0-8 mM). Filled hydrogel particles were fabricated as follows: (i) high methoxy pectin, sodium caseinate, and caseinate-coated lipid droplets were mixed at pH 7 under conditions where phase separation due to thermodynamic incompatibility occurred; (ii) this mixture was acidified (pH 5) to induce adsorption of anionic pectin molecules around lipid-filled caseinate-rich particles; (iii) the caseinate within the particles was enzymatically cross-linked using transglutaminase. Three mixing conditions (0, 100, and 1,000 rpm) were tested during particle acidification. Particle size measurements indicated that larger particles were formed at 0 and 100 rpm than at 1,000 rpm. Under high pH conditions (pH 6-8), particles cross-linked with transglutaminase remained intact while control particles (not cross-linked) disintegrated. The addition of calcium to both control and crosslinked particles resulted in system gelation above 4 mM calcium chloride. Control and cross-linked particles remained stable to heating and to the addition of sodium chloride. Results from this study demonstrate the versatility and robustness of this delivery system for lipophilic bioactives.