Background: Common marmosets have been widely used in biomedical research for years. Nutritional control is an important factor in managing their health, and insect intake would be beneficial for that purpose because common marmosets frequently feed on insects in natural habitats. However, the effect of insect feeding on the marmoset body has not been clearly characterized. Here, we examined the effect of enhanced insect feeding on the gut by analyzing the fecal microbiome and transcriptome of captive marmosets. Methods: A family consisting of six marmosets was divided into two groups. During the seven-day intervention period, one group (the insect feeding group, or Group IF) was fed one cricket and one giant mealworm per marmoset per day, while the other (the control group, or Group C) was not fed these insects. RNA was extracted from fecal samples to evaluate the ecology and transcriptome of the microbiome, which were then compared among time points before (Pre), just after (Post), and two weeks after intervention (After) by total RNA sequencing (total RNA-seq). Results: General health status was not changed throughout the experimental period in either group. Distinct changes were observed only in the microbiome of Group IF after the insect feeding treatment. A species of flagellate, Hypotrichomonas mariae , was identified for the first time in common marmosets, but only after enhanced insect feeding. The structure of the microbiome differed between the groups with and without insect feeding. There were significant changes in the transcriptome of Group IF only, and some of the changes in the transcriptome mirrored the fluctuations in the microbiome. Conclusions: Enhanced insect feeding modified the distribution of the fecal microbiomes of the marmosets, which were suggested to interact with the transcriptomes. The rapid changes in the microbiome and transcriptome are deeply connected to the feeding ecology of marmosets in the wild. The results were informative for identifying the physiological impact of insect feeding and for detecting transcripts that are currently unidentifiable. The present study supports a feeding regimen for captive marmosets that includes insects to maintain the natural balance of symbiotic metabolism in the gut microbiome.