Chemotherapy-induced cognitive impairment (CICI) is a poorly defined complication of chemotherapy treatment that has been recognised as a priority concern by cancer survivors, given the symptom burden and lack of therapeutic options. A growing body of anecdotal evidence suggests that the gastrointestinal microbiota may play a role in CICI development, through its influence over neuropathological events via the microbiota-gut-brain axis. However, the relationship between microbiota composition and CICI development has not been explored in a longitudinal study. Therefore, we aimed to longitudinally characterise the individual, dynamic shifts in gastrointestinal microbiota composition during chemotherapy treatment and identify pre- and post-treatment microbial signatures associated with the neurocognitive signatures induced by chemotherapy. Twenty-two women, newly diagnosed with breast cancer, each provided N=4 stool samples across the first two cycles of chemotherapy treatment for microbiota analysis using 16S. Time-matched data on neurocognitive and gastrointestinal symptoms were also provided using the Functional Assessment of Cancer Therapy – Cognitive Function version 3 (FACT-Cog) questionnaire and the Functional Assessment of Chronic Illness Therapy – Diarrhoea Subscale (FACIT-DS) respectively. The relative abundance of Burkholderiaceae was found to be significantly increased in individuals with cognitive impairment (p<0.0001), and strongly associated with both FACT-Cog (p<0.0001) and FACIT-DS (p=0.0017) total scores. This established that as Burkholderiaceae relative abundance increased, cognitive impairment and diarrhoea burden worsened. Akkermansiaceae was the taxon most significantly enriched in participants with no cognitive impairment (p=0.0308) but, this did not significantly correlate with FACT-Cog or FACIT-DS total scores. Although this study did not identify predictive, baseline microbial signatures of CICI, there was evidence of a triadic relationship present within the microbiota-gut-brain axis in women with breast cancer undergoing chemotherapy. Consequently, the role of microbial-targeted preventative or therapeutic measures for CICI warrants further investigation.