Maternally inherited endosymbionts are found in numerous insect species and have various effects on host ecology. New symbioses are most commonly established following lateral transfer of an existing symbiont from one host species to another. Laboratory study has demonstrated that symbionts commonly perform poorly in novel hosts, with weak vertical transmission and maladaptive pathogenicity being observed in the generations following transfer. This poor performance probably limits symbiont occurrence. We here use microarray technology to test whether poor symbiont performance observed following 1 year of vertical transmission through a new host is associated with alteration in host gene expression or whether it occurs independently of this. We utilize the Drosophila melanogaster—Spiroplasma interaction and test the response of the host in the presence of both natural Spiroplasma infections and novel Spiroplasma infections transinfected previously from other host species. None of the Spiroplasma infections investigated produced upregulation in host haemolymph/fat body-based immune responses, and we therefore rejected the hypothesis that failure to thrive was associated with immune upregulation. One infection was associated with a downregulation of genes associated with egg production compared to uninfected controls, indicative of damage to the host. The Spiroplasma infection showed that the weakest vertical transmission showed no significant disturbance to host gene expression compared to uninfected controls. We conclude that the failure of Spiroplasma in novel host species is associated either with causing harm to their new hosts or through a failure to thrive in the new host that occurs independently of host responses to infection.