The aim of this study was to prepare starch-based filled hydrogels fortified with a model lipophilic nutraceutical (β-carotene) and determine the influence of starch type (mung bean or rice starch) and surfactant type (whey protein isolate (WPI) or Tween 20 (T20)) on lipid digestibility and β-carotene bioaccessibility. Microstructure, lipid digestion, and β-carotene bioaccessibility were measured as the emulsions and filled hydrogels were passed through a simulated gastrointestinal tract that included oral, gastric, and intestinal phases. The bioaccessibility was defined as the fraction of β-carotene solubilized within the mixed micelle phase after lipid digestion. Non-encapsulated T20-stabilized emulsions had better aggregation stability than WPI-stabilized emulsions under simulated gastrointestinal conditions, which led to a higher β-carotene bioaccessibility. Both Tween 20- and WPI-stabilized emulsions incorporated in starch-based filled hydrogels led to high lipid digestion and β-carotene bioaccessibility. The release behavior of free fatty acids during lipase digestion depended on the type of starch used as a hydrogel matrix, which was attributed to differences in starch structure. The information obtained in this study may be useful for the fortification of starch-based gelled products with lipophilic nutraceuticals. Schematic diagram of filled hydrogel particles consisting of nutraceutical loaded lipid droplets incorporated within starch based hydrogels. Display omitted •Lipophilic nutraceuticals (β-carotene) were trapped in lipid droplets.•Fortified filled hydrogels were fabricated by mixing lipid droplets and starch gels.•The rate of lipid digestion depended on emulsifier and starch type.•Nutraceutical bioavailability also depended on emulsifier and starch type.•Filled hydrogels may be formulated to alter the gastrointestinal fate of lipids.