Intergenerational inheritance of transcriptional responses induced by low temperature rearing has recently been shown in Drosophila. Besides germline inheritance, fecal transfer experiments indirectly suggested that the acquired microbiome may also have contributed to the transcriptional responses in offspring. Here, we analyze expression data on inheritance of the cold‐induced effects in conjunction with previously reported transcriptomic differences between flies with a microbiota or axenic flies and provide support for a contribution of the acquired microbiome to the offspring phenotype. Also, based on a similar analysis in conjunction with diet‐ and metabolism‐related fly transcriptome data, we predicted and, then, experimentally confirmed that cold regulates triglyceride levels both inter‐ as well as trans‐generationally.