Background <p>Differences in the gut microbiome between lean and obese individuals, even twins, have been recognized for over a decade. The causative role of the microbiome in obesity is known from both mouse and human studies. In parallel, the gut microbiome has been implicated in the most common complications of pregnancy, including preterm birth, gestational diabetes mellitus, and gestational hypertension. Despite obesity being a well-established risk factor for these complications, the composition of the gut microbiome of obese pregnant individuals has not yet been studied. Here, we have examined the differences in the faecal microbiota between lean (<i>n</i> = 746) and obese (<i>n</i> = 254) pregnant women in Sweden, at two timepoints in pregnancy.</p> Results <p>The differences in the faecal microbiome of one thousand lean and obese persons persist during gestation. Obese individuals have a less diverse and less rich microbiome throughout all trimesters of pregnancy. In the first trimester, 9 species differ significantly between lean and obese individuals, and 35 in the early third trimester, after adjusting for confounders. However, only one species remained significant after further adjusting for bowel transit time, which differed significantly between lean and obese participants. Additionally, obese individuals harbored a consistently lower potential to produce propionate in their gut microbiomes, even after adjustments.</p> Conclusions <p>The faecal microbiome adapts to pregnancy with some key differences between lean and obese mothers, even in late pregnancy. Crucially, there is an over-abundance of opportunistic pathogens in the microbiome of obese pregnant women in the third trimester. This may be a potential underexplored mechanism explaining the increased rates of pregnancy complications among obese patients. Diet, probiotics, or medication interventions to correct the gut microbiome of pregnant obese individuals could potentially improve their pregnancy outcomes.</p>