Remote Indigenous Australians experience disproportionately poor cardio-metabolic health, which is largely underpinned by adverse dietary intake related to social determinants. Little evidence exists about the community environmental-level factors that shape diet quality in this geographically isolated population group. This study aimed to explore the modifiable environmental-level factors associated with the features of dietary intake that underpin cardio-metabolic disease risk in this population group. Community-level dietary intake data were estimated from weekly store sales data collected throughout 2012 and linked with concurrent social, built, and physical environmental dimension data for 13 remote Indigenous Australian communities in the Northern Territory. Statistical analyses were performed to investigate associations. At the community level, store sales of discretionary foods were lower in communities with greater distance to a neighbouring store (r = −0.45 (p < 0.05)). Sales of sugar-sweetened beverages were lower in communities with higher levels of household crowding (r = −0.55 (p < 0.05)), higher levels of Indigenous unemployment (r = −0.62 (p = 0.02)), and greater distance to neighbouring stores (r = −0.61 (p = 0.004)). Modifiable environmental-level factors may be associated with adverse diet quality in remote Indigenous Australian communities and further investigations of these factors should be considered when developing policies to improve dietary intake quality in geographically isolated populations.