The intensification of gilthead seabream (Sparus aurata) aquaculture highlights the need to develop sustainable strategies that reduce reliance on antibiotics. Antimicrobial peptides (AMPs), such as piscidins, represent a promising alternative to antibiotics; however, their effects on digestive physiology remain to be evaluated. This study assessed the effects of dietary supplementation with gilthead seabream synthetic piscidin 1 on the activity of digestive enzymes in this fish species and determined a potential dose-dependent response associated with this antimicrobial peptide. Following a 15-day acclimation period, 36 gilthead seabream juveniles (initial weight: 35.16 ± 1.45 g) were randomly distributed into six 250 L tanks (N = 6 fish/tank). A 17-day in vivo feeding trial was conducted using three experimental diets, including a control (0%), low dose (0.05%), and high dose (0.1%) of piscidin 1, which was protected using carrageenan, pectin, and chitosan microparticles. Following the experimental period, pyloric caeca and intestinal samples were collected to determine specific enzyme activity (mU/mg protein) via spectrophotometric kinetic assays, and soluble protein was quantified using the Bradford assay. In the pyloric caeca, the high dose of piscidin 1 (0.1%) significantly reduced the specific activities of trypsin and chymotrypsin (p < 0.05). In the intestine, trypsin activity remained stable across all treatments, whereas chymotrypsin activity significantly decreased in the group fed the low dose (0.05%). In contrast, aminopeptidase and alpha-amylase activities showed no significant differences among the treatments in any of the analysed tissues (p < 0.05). In conclusion, dietary supplementation with piscidin 1 selectively reduced the levels of certain proteolytic enzymes, especially trypsin and chymotrypsin. The stability of aminopeptidase and α-amylase suggests that piscidin 1 does not cause a generalised alteration of digestive function, nor does it significantly affect the final digestion of peptides and carbohydrates. Overall, piscidin 1 supplementation could lead to a partial reduction in the initial stages of protein digestion, although growth data, feed utilisation, and digestibility are required to determine whether these changes have significant nutritional effects.