Incorporating natural antimicrobial agents into food systems is a promising alternative to synthetic additives. This study developed corn-based functional extrudates enriched with essential oils from oregano, rosemary, chamomile, and hypericum (EOB) via twin screw extrusion processing. EOB was introduced in both encapsulated and non-encapsulated forms using electrohydrodynamic processing, spray drying, and freeze drying within a whey protein isolate and pullulan matrix. Extrudates containing spray-dried EOB (SP-EOB) achieved the highest extrusion efficiency (72.94% ± 1.16%). Morphological analysis revealed homogeneous structures for XE and XS extrudates, while XF extrudates were more porous. The gastrointestinal release kinetics of EOB from the extrudates were best described by the Korsmeyer-Peppas model, indicating an anomalous diffusion mechanism with “n” values ranging from 0.480 to 0.650. These findings highlight the potential for naturally bioactive and sustainable food products via advanced processing methods, reducing dependence on synthetic additives.