Fish consumption rose sharply in last decades, together with fishing levels, leading to dramatic consequences on marine habitats. Aquaculture represents a sustainable and secure fish supply and it has confirmed as the fastest growing food production sector. In the search of sustainable and high-performing fish meal (FM) and fish oil (FO)-free formulations, insect meal (IM) and poultry by-product meal (PBMs) formulations have been proposed as candidate animal protein source for their inclusion in fish feeds. The aim of the present study was to investigate the effect of partial replacement of vegetable proteins with IM and PBM in rainbow trout (Oncorhynchus mykiss) feed formulation on gut health by focusing on microbiota composition and markers of oxidation and gut barrier integrity. 1200 juvenile of rainbow trout were fed for 3 months with eight different dietary treatments, where different percentage of Hermetia illucens meal or PBM were used to replace FM and vegetable ingredients (VM). Test diets showed good growth performances compared to both control FM and VM formulation. Gut microbiota composition through 16S rRNA analysis revealed that Hermetia inclusion in meal increased the alpha diversity and led to a significant increase of chitin degrader genera Actinomyces and Bacillus. High-throughput sequencing of feeds pellet revealed some analogies between gut microbial sequences and those in feed formulations containing Hermetia illucens, supporting the hypothesis of feed-borne microbiota. The gene expression of IL-1B, IL-10, TGF-b, COX-2 and TCR-b in midgut and head kidney biopsies of fish, together with the plasma LPS analysis, revealed that none of the experimental diets had a deleterious impact on the overall immune health of the animals. Accordingly with our findings, both IM and PBM formulations could be considered as valid alternatives to VM and FM in the aquaculture practice.