Sceloporus occidentalis can be difficult to rear in the laboratory despite maintaining robust populations in nature, with individuals frequently dying at 4–6 weeks post-hatching. We hypothesize that this high mortality results from captive-reared individuals failing to acquire important components of their gut microbiome that they typically acquire by consuming natural substrate or adult fecal material in the wild. To test this hypothesis, we reared S. occidentalis hatchlings in a two-by-two factorial design varying exposure to adult fecal material and natural substrate. We then measured survival and phenotype (SVL, Mass, TL) at four ages: 0 days, 7 days, 14 days, and 30 days post-hatching. Contrary to our predictions, treatment did not affect hatchling survival. Post-hatching survival was uniformly poor across all four treatments suggesting a lack of microbes or other vital factors in adult feces or natural substrate cannot explain high captive mortality. However, hatchling phenotype was affected by the treatments at 14 days post-hatching with animals exposed to feces or substrate generally being in better condition. This effect disappeared by 30 days post-hatching possibly due to diminishing sample sizes. To further explore this effect, we used 16S rRNA sequencing to characterize the microbial community within the guts of hatchlings from our experiment and wild-caught adults, as well as substrates and feeder insects. These data will allow us to elucidate the extent to which treatments affected the gut microbiome of hatchlings and what the primary sources of the gut microbiome are for this species.