Juvenile queen conch are primarily associated with native seagrass such as Thalassia testudinum in large parts of their range in the Caribbean and the southern Gulf of Mexico. Here, a number of non-native seagrass species have been introduced including Halophila stipulacea, which is natural to the Red Sea and the Indo-Pacific. In the Caribbean, H. stipulacea often creates dense continuous mats with little or no sediment exposed, compared to native seagrass, which grows much less dense. We examined the diet and growth of juvenile conch in both native, mixed, and invasive seagrass beds using stable isotope analysis and an in situ growth enclosure experiment. Organic material in the sediment (i.e. benthic diatoms and particulate organic matter) was found to be the most important source of carbon and nitrogen for juvenile queen conch in all 3 habitats investigated, and there was a significantly higher probability of positive growth in the native seagrass compared to the invasive seagrass. Due to the importance of the organic material in the sediment as a source of nutrition for juvenile conch, limited access to the sediment in the invasive seagrass can potentially cause inadequate nutritional conditions to sustain high growth rates. Thus, it is likely that there is a negative effect on juvenile queen conch growth currently inhabiting invasive seagrass beds, compared to native seagrass beds, when other potential sources of nutrition are not available.