Add sliced onions to a medium bowl. Pour enough boiling water over onions so that they are covered. Count to 5 then drain. Add the onions to glass jars (or a food safe glass container with lid).
Toast cinnamon, cloves, and the red pepper flakes until fragrant in a small saucepan over medium heat, 3 to 5 minutes. Whisk in the vinegar, lime juice, 3 tablespoons of the sugar, and salt.
Bring to a simmer and cook until the sugar and salt have dissolved, 1 to 2 minutes. Taste for sweetness then add more sugar as needed.
Pour brine over the onions. Allow to stand at room temperature until cooled. Serve or cover and refrigerate 2 to 3 weeks.
