Poor diet has been identified as a major cause of chronic disease. In this study we estimated the 2018 economic burden of chronic disease attributable to not complying with Canadian food recommendations. We retrieved the chronic disease risk estimates for intakes of both protective (fruit, vegetables, milk, whole grains, nuts and seeds) and harmful foods (sugar-sweetened beverages, processed meat, red meat) from the Global Burden of Disease Study, and food intakes from the 2015 Canadian Community Health Survey 24-hour dietary recalls (n = 19,797). Population attributable fractions (PAFs) were calculated for all food-chronic disease combinations, and mathematically adjusted to estimate the 2018 annual direct (hospital, physician, drug) and indirect (human capital approach) economic burden for each disease. Not meeting the eight food recommendations was estimated to be responsible for CAD$15.8 billion/year in direct (CAD$5.9 billion) and indirect (CAD$9.9 billion) costs. The economic burden of Canadians under-consuming healthful foods exceeded the burden of overconsumption of harmful foods (CAD$12.5 billion vs. CAD$3.3 billion). Our findings suggest poor diet represents a substantial economic burden in Canada. Interventions may be more effective if they are wide in focus and promote decreased consumption of harmful foods alongside increased consumption of healthful foods, with emphasis on whole grains and nuts and seeds.