Place the ingredients for the cups, minus the flaky sea salt, in a medium bowl and mix to combine. Divide the mixture between 8 muffin cups.
Transfer to the freezer and freeze for 30 minutes.
Place the chocolate chips and the almond butter in a small pot over low heat. Cook just until melted and combined.
Pour the mixture over the granola cups, sprinkle with flaky sea salt, and return to the freezer for at least one hour before placing in a lidded container. Store refrigerated for up to one week.