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ABSTRACT Accumulating evidence supports the role of microbiota in autoimmune processes, but research regarding the role of the gut microbiota in celiac disease (CD) is still emerging, and a consistent CD-associated dysbiosis pattern has not yet been defined. Here, we characterized the microbiota of children newly diagnosed with CD, with their unaffected family members as a healthy control group to reduce confounding factors including genetic background, hygiene, dietary habits, and environment, and followed children with CD over 1 year of dietary intervention (exclusion of gluten) to understand if the microbiota is associated with CD and its mediation. We did not find differences in the microbiota of siblings with and without CD, despite a wealth of evidence in the literature supporting CD-specific microbiota. CD is common among first-degree relatives, so this could suggest that unaffected family members in this study may be living in a pre-CD state, currently below clinical detection. Interestingly, despite the effectiveness of diet in CD control, we did not observe diet-mediated microbiota changes, except for short-term increase in Akkermansia muciniphila. This lack of effect could suggest a very strong CD microbial signature even when controlled or could be a technical shortcoming. Expanded future studies with both related and unrelated controls and diet interventions in both the CD and control arms can provide further context to our findings. IMPORTANCE The microbiota is the community of microbes that live in and on us. These microbes are essential to our health and everyday function. Disruption of the community is associated with diseases ranging from metabolic syndrome to autoimmune diseases to mental disorders. In the case of celiac disease (CD), research remains inconclusive regarding implications of the microbiota in etiology. Here, we compared microbiota of children with CD to those of their unaffected family members and found very few differences in microbiota profiles. We next examined how gluten elimination in CD patients affects the microbiota. Surprisingly, despite diet adherence, microbiota shifts were minimal, with only a short-term increase in Akkermansia muciniphila. Previous studies suggest that family members of CD patients may be living in a pre-CD state, which could explain their microbial similarity. A larger study with unrelated controls and increased microbiota monitoring during diet intervention should give our findings more perspective.