Heat a non-stick skillet over medium heat; cook and stir onion and garlic in the hot skillet until fragrant and onion is slightly softened, 5 to 10 minutes. Stir blueberries into onion mixture and cook for 2 to 3 minutes.
Add lemon zest, lemon juice, agave nectar, ginger, cinnamon, and salt to blueberry mixture; cook and stir until chutney is thickened, 10 to 15 minutes. Refrigerate until chilled, at least 30 minutes.