Clostridium perfringens is a commensal, but also an opportunistic pathogen that can lead to lethal diseases as a result of overgrowth when homeostasis is disrupted. The current course of treatment is antibiotics. However, with increasing antibiotic resistance alternatives are required. We investigated the antimicrobial capacity of digest from different black soldier fly- and mealworm-derived fractions towards C. perfringens by using in vitro models. Culturing C. perfringens with digest of insect-derived fractions showed that fractions containing black soldier fly larvae protein significantly (p < 0.05) inhibited the growth of C. perfringens. In relation to this effect, many small (<5 amino acids) anti-microbial peptides were identified. The impact on healthy microbiota was also investigated through 16S rRNA sequencing and SCFA secretion following exposure of healthy faecal-derived microbiota to digests. This revealed a small but significant (p < 0.05) reduction in abundance and diversity of microbiota, mainly a result of a strong reduction in Firmicutes (e.g. Enterobacter) and increased abundance of Proteobacteria (e.g. Klebsiella). These changes coincided with increased levels of acetic, propionic, and butyric acid secretion. The combined impact of black soldier fly larvae protein on these in vitro assays suggest it can be a promising additional tool to combat C. perfringens infection.