Honey bees are highly important pollinators in agroecosystems, but they are currently under growing environmental pressures (e.g., from pesticides, poor nutrition, and parasites). Due to the multiplicity of environmental stress factors, their protection requires diverse and integrative approaches. Among those is the development of immunomodulatory tools, as immunosuppression is often observed in stressed bees. Toward this goal, the use of exogenous bacteria with immunomodulatory potential has recently been investigated, but knowledge about the potential of honey bee endogenous bacteria is limited. We therefore tested the influence of single strains of five species of endogenous lactic acid bacteria strains on the bee immune system during the larval stage. We measured the expression level of seven immune-related genes and the gene encoding the storage protein Hexamerin 70b. Two of the strains induced an immune stimulation, but this was limited to the antimicrobial peptide Apidaecin1. Upregulation of Apidaecin1 was associated to the downregulation of Hexamerin 70b. Those results suggest that the bee response to endogenous bacteria is specific both at the species and immune levels. As immune responses are costly, this specificity may be adaptive for saving energy and avoiding any negative side effects on the host development or survival. Further screening of bacteria immunomodulatory potential is needed, but associated immune cost needs to be taken into account for improving honey bee resilience to environmental stress.