Endosymbionts are prominent members of tick microbiota. They have various consequences for the biology of their arthropod host, being involved in their nutrition and development by supplying vitamins that are essential for tick survival or in vector competence for example. Candidatus Midichloria mitochondrii is the main endosymbiont of the predominant tick in Europe, Ixodes ricinus. This alphaproteobacterium resides mainly in the tick ovarian cells and exhibits a peculiar intramitochondrial tropism. It is also vertically transmitted and infects virtually all females of I. ricinus. Unlike known examples of other tick-endosymbiont couples, the nature of the mutualistic association between I. ricinus and M. mitochondrii has not been formally characterized to date. To decipher the influence of M. mitochondrii on the gene expression of its tick host, we compared the transcriptome of two strains of I. ricinus. The first tick strain was recently sampled from the wild (WT) and harbored high load of Midichloria. In contrast, the second strain (Lab), reared under laboratory conditions for ca. 30 generations, has lost the endosymbiont — which cannot be detected molecularly. Using RNA-seq, we characterized differentially expressed (DE) genes between WT and Lab female ticks at before engorgement — Day 0 — and at the end of the slow-feeding stage — Day 4). We first assembled a high-quality de novo transcriptome of 36,499 contigs. Statistical analysis showed twice as many DE genes at D0 compared to D4 (e.g., 1,148 vs. 521 for the overexpressed genes, 240 being common for both time points). For both time points, the gene with the highest fold-change encoded an antimicrobial peptide, ricinusin, whose overexpression could have been induced by triggering one of the signaling pathways of the tick innate immune system. Gene Ontology (GO) enrichment analysis revealed at both D0 and D4 terms related to the mitochondrial inner membrane and intermembrane space. At D4, GO terms related to tick immune system were enriched, while at D0, the GO term ‘heme binding’ could be correlated with M. mitochondrii heme synthesis ability and thus its potential supply during the tick off-host periods.