L-Carnitine, sourced from red meat, dairy, and endogenous synthesis, plays a vital role in fatty acid metabolism and energy production. While beneficial for cardiovascular, muscular, and neural health, its interaction with the gut microbiota and conversion into trimethylamine (TMA) and trimethylamine N-oxide (TMAO) raise concerns about heart health. TMAO, produced through the gut-microbial metabolism of L-carnitine and subsequent liver oxidation, is associated with cardiovascular risks, including atherosclerosis, heart attacks, and stroke. It contributes to cholesterol deposition, vascular dysfunction, and platelet aggregation. Omnivorous diets, rich in L-carnitine, are associated with higher TMAO levels compared to plant-based diets, which are linked to lower cardiovascular disease risks. Dietary interventions, such as increasing fiber, polyphenols, and probiotics, can modulate the gut microbiota to reduce TMAO production. These strategies seek to balance L-carnitine’s benefits with its potential risks related to TMAO production. Future research should focus on personalized approaches to optimize L-carnitine use while mitigating its cardiovascular impacts, exploring microbial modulation and dietary strategies to minimize the TMAO levels and associated risks.