Hsp90 is a molecular chaperone involved in the regulation and maturation of kinases and transcription factors. In C. elegans Hsp90 participates in the development of fertility, maintenance of muscle structure and the regulation of stress response and dauer state. To understand the consequences of Hsp90-depletion we studied Hsp90 RNAi-treated nematodes by DNA microarrays and mass spectrometry. We find that upon development of phenotypes the levels of chaperones and cofactors are increased, while specific proteins related to the innate immune response are specifically depleted. We further uncover Hsp90-dependent signatures of gonad development and larval development. Using reporter strains for the responsive genes skr-5, dod-24 and clec-60, we confirm an influence on the innate immune response in intestinal tissues, while alterations to development become evident in strains reporting on the presence of ZIP-8, CAV-1 and SEPA-1 in the gonad arms and very early embryos. These observations add molecular details to the Hsp90-dependent processes during development and stress responses and imply that multiple interactions of this chaperone system are relevant for the nematode’s life and development.