Although antimicrobial peptides (AMPs) have been used as feed additives, only a few studies have examined their use in ruminants. In this study, we evaluated the use of AMPs(recombinant swine defensin and a fly antibacterial peptide were mixed by 1:1) as a medicated feed additive for juvenile goats. Dietary treatments included control groups (group I: 300 g concentrate; group III: 600 g concentrate), and AMP-supplemented groups (group II: 300 g concentrate + 3.0 g AMPs; group IV: 600 g concentrate + 3.0 g AMPs). AMP-treated groups exhibited an increase in bacterial genera, including Fibrobacter, Anaerovibrio, and Succiniclasticum, and the ciliate genus Ophryoscolex; as well a reduction in bacterial genera, such as Selenomonas, Succinivibrio, and Treponema, and the ciliate genera Polyplastron, Entodinium, and Isotricha. The changes in Fibrobacter, Anaerovibrio, Ophryoscolex, Polyplastron, Entodinium, and Isotricha were related to the concentrate. AMP treatment led to increased body weight, average daily weight gain, enzymatic activity (pectinase, xylanase, and lipase), especially in the normal concentrate group, and influence on ruminal fermentation function. In addition, goats treated with AMPs had higher rumen microorganism diversity indices than the control groups. Our results demonstrate that AMPs can be utilized as feed additives for juvenile goats.