Most surfaces are colonized by microorganisms that form interactive and fluctuating communities, commonly referred to as the ‘microbiome.’ To effectively sample the microbiome, different methods are employed depending on the tissue or surface type. Although most vertebrates are oviparous, little is known about how microorganisms are represented on eggs, particularly those of non-avian reptiles. Using three different experiments, our primary goal was to develop methods to effectively sample and manipulate the eggshell microbiome of reptiles, as well as to minimize contamination from external sources. We employed two different egg microbiome sampling methods (sonication vs. swabbing) on lizard (Anolis sagrei) eggs and elucidated bacterial taxa using 16S rRNA gene-sequencing. We also assessed the efficacy of ethanol and bleach in reducing bacterial communities on the eggshell and their influence on egg survival. Lastly, to sample the maternally-derived eggshell microbiome (minimizing contamination from nesting substrate), we attempted to hormonally-induce oviposition in sterile conditions. We found that swabbing provided similar abundance and diversity measurements as sonication, but these sampling techniques differed in terms of bacterial community structure. Bacterial community load was reduced using 70% ethanol and 20% bleach. Additionally, ethanol greatly reduced egg survival while bleach did not. Lastly, we could not successfully induce oviposition in A. sagrei using previously described methods in the literature, thus future experiments that examine effects of different hormones on oviposition are warranted. Overall, our results provide useful guidelines for future studies that examine the source and function of the eggshell microbiome.