Lycopene is claimed to have numerous physiological benefits, but its poor water solubility, chemical instability, and low bioavailability limit its application in functional foods and health care products. In this study, lycopene-loaded emulsions containing oil droplets with different interfacial structures were prepared and then cross-linked using transglutaminase (TG) and/or calcium ions (Ca2+) to form emulsion gels. The oil droplets were first coated by interfacial layers comprised of whey protein isolate (WPI) and sodium alginate (SA). During emulsion preparation, the SA was added either before or after homogenization to create complex or layer-by-layer coatings, respectively. Subsequently, TG and Ca2+ were used to cross-link WPI and SA to form emulsion gels. The results show that double-crosslinking increased the gel strength and viscosity of the emulsion gels. The layer-by-layer emulsion gels were stronger and more viscous than the complex ones. The photochemical and gastrointestinal stability of lycopene encapsulated within the emulsion gels was higher than that of free lycopene. An MTT toxicity test showed that the emulsion gels exhibited no cytotoxicity to Caco-2 cells. The lycopene-loaded emulsion gels exhibited stronger anti-inflammatory activity on the Caco-2 cells than the control. In addition, the absorption of lycopene by the Caco-2 cells increased after encapsulation. This study provides a new approach of preparing edible soft materials to enhance the application of hydrophobic bioactives (like lycopene) in functional foods. Display omitted •Emulsions were formed containing oil droplets with layer-by-layer or complex coatings.•These emulsions were then gelled by crosslinking with transglutaminase and/or Ca2+.•The layer-by-layer emulsion gels exhibited better functional properties.•The double-crosslinked emulsion gels improved the stability of lycopene.•The emulsion gels increased the bioaccessibility and bioactivity of lycopene.