Cut the top and bottom of the orange. Quarter the orange. Remove the peel as seamlessly as possible.
Cut each peel into three thin strips.
Bring the two cups of water to boil and reduce the heat to medium. Cook peels in boiling water for 15 minutes.
Scoop out peels with a slotted spoon. Add two cups of sugar to simmering water. Stir until dissolved.
Add the peels and reduce the heat to medium-low. Simmer the peels in the syrup reduction for 45 minutes to 1 hour.
Add remaining one cup of sugar to a baking sheet. Scoop peels with a slotted spoon onto a paper towel to soak up wetness.
Add peels to baking sheet and coat well with sugar. You'll want to be sure the peels are more dry than wet to prevent the sugar from clumping.
Place the peels on a cooling rack and let sit until the coating is dry, around 1-2 days.
When dry, melt chocolate chips in a small saucepan. Drizzle chocolate over candied orange peels set on a parchment paper-covered baking sheet. Sprinkle sea salt flakes over peels as preferred.
Refrigerate up to 1 hour. Serve!