Inulin is generally considered safe, and the main side effects are gastrointestinal in nature due to the gas produced during bacterial fermentation. Possible side effects include flatulence, abdominal rumbling or cramping, bloating, and diarrhea.[1][2] These side effects may be worse at higher doses and with short-chain inulin (oligofructose, FOS) due to faster fermentation rates.[2] Starting at a lower dose and increasing slowly over time can help to improve tolerance.[1]
One major limitation of inulin is how variable its effect can be between individuals. Many of the potential benefits of inulin are due to its interactions with the gut microbiome, but the microbes in the gut can vary greatly between different people, which could lead to inconsistent and unpredictable effects.[1] A study in mice found that after six months of consuming a high-fat diet (intending to mimic a Western diet) enriched with inulin, most mice developed liver damage and liver cancer, which seemed to be related to the production of secondary bile acids by certain gut bacteria. The authors suggested that the health effects (both positive and negative) of fermentable fibers may depend on the unique gut microbial environment. Importantly, the amount of inulin consumed daily in this study was not clear, and this negative effect has not been observed in human clinical trials.[3]