Haudenosaunee Peoples of eastern North America have a strong agricultural tradition and culture associated with maize horticulture. Traditional foodways and diet were disrupted after the people were dispossessed from traditional lands maintained prior to colonization. As a result, Haudenosaunee have been disconnected from their traditional diet and lifestyle, and chronic diseases such as diabetes and obesity are increasing. Healthy Roots was developed in Six Nations of the Grand River territory by Haudenosaunee community members. It started as a 90-day challenge, in which participants adhere to a diet of traditional foods found in Haudenosaunee territories pre-European contact. The community decided to formally evaluate the impact of the diet in a pilot pre–post intervention study of 22 participants in 2016/17. We investigated the effects of the 3-month dietary intervention on physical measurements, ectopic fat (including visceral and liver adipose tissue), serum lipids, and hemoglobin A1c among Haudenosaunee participants in Six Nations. We provided biweekly Haudenosaunee food boxes, and offered workshops, cooking classes, and individual support from a dietitian. The intervention reduced body weight, body circumferences including waist circumference, hemoglobin A1c, and MRI-detected hepatic fat fraction. There were no adverse events. Engagement in the program was high and trends favoured improved well-being. The intervention shows great potential as a mechanism for improving physical health and restoring cultural connectedness and identity. The implications for improving mental health and community cohesion are also important areas to consider in future research.