The gastrointestinal (GI) microbiome is considered an additional organ of the human body that is implicated in health and disease (1). Dietary intake is a major modifiable variable contributing to microbial colonisation and fermentation (2). Advancements in microbial sequencing methods and interest in the impact of microbiome on health and disease have led to an exponential increase in studies investigating relationships between diet and the GI microbiome. However, high-quality synthesis of research is limited by considerable heterogeneity in methods used to assess and analyse dietary intake, sequence microbiome data and subsequently analyse diet-microbiome associations. This scoping review aimed to synthesise dietary and microbiome assessment and analysis methods used in human studies that investigate diet-microbiome taxonomic associations, and establish guidelines to inform future research methodology. A systematic literature search identified papers that measured individual-level dietary intake in humans and sequenced GI microbiome using either 16S rRNA or metagenomic shotgun sequencing. Studies were required to investigate associations between dietary intake and some aspect of GI microbiome. Databases searched were MEDLINE, EMBASE, CINAHL, Cochrane and Google Scholar, resulting in 22,228 unique records after de-duplication. After full-text screening, 1,262 relevant articles were identified, then further categorised based on study methods. Additional data were extracted from a subset of 295 studies that captured whole dietary intake and compared this with GI microbiome. Twenty-three percent of included diet-microbiome studies employed comprehensive methods to capture whole dietary intake for analysis with taxonomic microbiome data. The remainder of studies captured a single food, nutrient, or looked at compositional microbiome rather than taxonomy. Within the comprehensive subset, there were 84 different variations of food frequency questionnaires (FFQ), 12 alternative surveys, and 4 types of diet recalls or diaries capturing between 1 and 14 days of dietary intake. Fifty-five percent (n=163) of studies investigated habitual dietary intake, 35% (n=101) investigated recent dietary intake, and 10% (n=30) assessed both. Eighty-one percent of studies employed 16S rRNA sequencing, with wide variation in extraction, sequencing, pre-processing and annotation methods. There were also substantial gaps in reporting of methods for each step of the process, limiting further comparison or consolidation of study outcomes. Microbiome-specific statistical methods were only used in 11% of the identified subset, with preference for correlational methods not well-suited to handling the complexities of microbiome data (3). Only eight studies in this review had both raw dietary and sequencing data deposited in online repositories, limiting future validation and comparison of results. This review reveals the extent of the inconsistencies that exist in exploratory diet-microbiome studies, despite published recommendations to assist researchers in these processes (4). Collaborative efforts towards consensus methods and reporting will help to substantially progress the diet-microbiome research field towards high-quality evidence and meta-analyses.