Food insecurity affects the health of college-aged individuals, but its impact on the gut microbiome (GM) over time is poorly understood. This study explored the association between food insecurity and the GM in 85 college students, identifying microbial taxa, metabolites, and pathways linked to food security status and examining GM stability and microbe-metabolite interactions. Longitudinal GM and metabolomic data were collected from first-year students over an academic year, encompassing periods of variable food security status. Participants were categorized into three groups: food insecure (FI, n=13), food secure (FS, n=44), and variable (VAR, n=28) status. GM composition varied significantly between FS classifications (Bray-Curtis dissimilarity, P ≤ 0.005). Stability analysis revealed correlations between stability scores and microbial features, pathways, and metabolites. Specific microbes (e.g., Bifidobacterium species, Faecalibacterium prausnitizii D, and Lachnospiraceae), pathways (energy and microbial turnover), and metabolites (cadaverine, N-acetylcadaverine, putrescine, testosterone sulfate, and creatine) associated with FI status were identified. Multi-omic integration revealed metabolic pathways influenced by differentially abundant microbial species and co-occurring fecal metabolites in food-insecure participants related to the microbial production of polyamines, detoxification, and energy metabolism. The transition from FS to FI showed no significant differences at specific taxonomic, functional, or metabolite levels. This study uncovers complex interactions between food security, GM composition, and metabolism. Significant differences were found in microbial community variability and metabolic pathways associated with food security status, but the transition from food security to insecurity disrupted the GM without clear taxonomic or functional distinctions, emphasizing the need for further research into these mechanisms.