© 2019 The Author(s). Background: Metabolic disorders (e.g., impaired glucose tolerance, insulin resistance, and type 2 diabetes) are more prevalent in people with spinal cord injury (SCI) than able-bodied individuals. Dietary modification is a more cost-effective treatment option than pharmacological therapies for reducing the risk of metabolic dysfunction. Lowering carbohydrate, increasing protein, and maintaining a proper dietary fat intake are expected to induce favorable adaptations in glucose control, body fat distribution, and the composition of the gut microbiome. However, dietary modification has not been rigorously investigated in people with SCI. The purpose of this study is to determine if an 8-week low-carbohydrate/high-protein (LC/HP) dietary intervention will show improvements in clinically important metrics of metabolic function, body composition, the composition of gut bacteria, and quality of life. Methods/design: We intend to recruit 100 participants with chronic traumatic SCI (3 years postinjury, C5-L2, American Spinal Injury Association impairment scale A-D, and aged 18-65 years) and insulin resistance, impaired glucose tolerance or untreated type 2 diabetes and randomly assign them to an 8-week LC/HP dietary intervention group or a control group. The daily LC/HP dietary intervention includes ~ 30% total energy as protein (1.6 g/kg per day) with a carbohydrate-to-protein ratio < 1.5 and fat intake set at ~ 30% of the total energy intake. The control group does not receive any dietary intervention and are continuing with their regular daily diets. Glucose tolerance, insulin sensitivity, β-cell function, body composition, gut microbiome composition, and quality of life measures are assessed at week 1, before starting the LC/HP dietary intervention, and at week 8, after completion of the LC/HP dietary intervention. Discussion: New information derived from this project will result in the development of a low-cost, simple, self-administered LC/HP dietary intervention for improving metabolic function in individuals with chronic SCI, improved understanding of the composition of gut bacteria in SCI, and how a LC/HP dietary intervention alters gut bacteria composition. In addition, this project will improve our understanding of the relationship between metabolic function and quality of life in individuals with long-standing SCI. Trial registration: ClinicalTrials.gov, NCT03207841. Registered on 5 June 2017.