In this study, we explore how myxozoan parasites modulate the host proteome landscape and immune responses at the target organs, thereby determining the outcome of co-infections in rainbow trout. Kidney and head cartilage samples were collected from five fish groups. In group 1, fish were infected with M. cerebralis (Mc), while fish in group 2 were exposed to T. bryosalmonae spores (Tb). Thirty days after infection, half of the fish from group 1 and group 2 were reciprocally co-infected with the other parasite, establishing group 3 (Mc+) and group 4 (Tb+). Group 5 fish were mock exposed to specific pathogen-free water and used as a negative control (C). In the head cartilage, upregulated proteins are involved in signal transduction, immune response, and host protection against oxidative stress, while the downregulated molecules are associated with cytoskeleton organization, DNA and RNA repair, protein folding, and metabolism. In the kidney, upregulated proteins are mainly involved in signal transduction, host immunity, DNA and RNA repair, and protection against oxidative stress. The downregulated proteins are mainly associated with extracellular matrix (ECM), cytoskeleton organization, and metabolism. This study provides the first proteomic profiles of rainbow trout responses to single and co-infections with M. cerebralis and T. bryosalmonae at the target organs. It delivers key information on how these two parasites trigger distinct immune signaling pathways and enhances our understanding of the host myxozoan interactions in single and co-infections, potentially enabling the development of effective interventions and therapeutic strategies for WD and PKD management in salmonid aquaculture.