We assessed public perspectives of microbiome research privacy risks before and after a nationwide emergency was declared in the United States regarding the Covid-19 pandemic. From January to July of 2020, we conducted an online survey of perceived privacy risks of microbiome research among U.S. adults. Among 3,106 participants (the preemergency group), most expressed that the microbiome posed privacy risks similar to those associated with DNA (60.3%) or medical records (50.6%) and that they would prefer detailed explanations (70.2%) of risk in consent materials. Only 8.9% reported moderate to high familiarity with microbiome privacy risks. In adjusted analyses, individuals who participated in the study after the Covid-19 emergency was declared (the Covid-19 emergency group) were less likely to express that microbiome privacy risks were similar to those of DNA or medical records and more likely to report familiarity with the privacy risks of microbiomes. There was a trend toward increased concern after the Covid-19 emergency was declared (p = 0.053). Overall, the study revealed that many U.S. adults believe that microbiome privacy risks are similar to those associated with DNA or medical records, and they prefer detailed explanations in consent documents. Individuals who participated after the Covid-19 emergency was declared reported greater knowledge of microbiome privacy risks but had more concern. KEYWORDS human subjects research, human research ethics, privacy, research data privacy, microbiome research, microbial genetics, Covid-19