Pectins are plant polysaccharides consumed as part of a diet containing fruits and vegetables. Inside the gastrointestinal tract, pectin cannot be metabolized by the mammalian cells but is fermented by the gut microbiota in the colon with the subsequent release of end products including short-chain fatty acids (SCFA). The prebiotic effects of pectin have been previously evaluated but reports are inconsistent, most likely due to differences in the pectin chemical structure which can vary by molecular weight (MW) and degree of esterification (DE). Here, the effects of two different MW lemon pectins with varying DEs on the gut microbiota of two donors were evaluated in vitro. The results demonstrated that low MW, high DE lemon pectin (LMW-HDE) altered community structure in a donor-dependent manner, whereas high MW, low DE lemon pectin (HMW-LDE) increased taxa within in both donors. LMW-HDE and HMW-LDE lemon pectins both increased total SCFAs (1.49- and 1.46-fold, respectively) and increased acetic acid by 1.64-fold. Additionally, LMW-HDE lemon pectin led to an average 1.41-fold increase in butanoic acid. Together, these data provide valuable information linking chemical structure of pectin to its effect on the gut microbiota structure and function, which is important to understanding its prebiotic potential.