Preheat the oven to 375°F (190°C). Line a baking sheet with parchment paper or a silpat.
Spread 1/2 cup raw almonds in a single layer on the prepared baking sheet. Roast 10–12 minutes until fragrant, watching closely so they do not burn.
While the almonds roast, in a small bowl combine 3 tablespoons freshly ground coffee beans, 1/2 tablespoon unsweetened cocoa powder, and 1/2 teaspoon sea salt. In a second small bowl combine 1 tablespoon melted coconut oil and 1 teaspoon vanilla extract.
Remove the almonds from the oven. Toss the hot almonds with the coconut oil + vanilla mixture, then toss immediately with the coffee–cocoa mixture so the almonds are evenly coated.
Return the coated almonds to the baking sheet and roast another ~10 minutes, until the coffee is fragrant and the almonds are starting to crisp. Remove from the oven and let cool completely.
Line a second baking sheet with parchment paper or a silpat and set aside.
In a microwave-safe bowl, combine 1 cup creamy peanut butter and 1/2 cup honey. Microwave for 30 seconds, then stir until smooth. Stir in the remaining 1 teaspoon vanilla extract.
In a medium mixing bowl, combine 2 1/4 cups old fashioned oatmeal, 1/2 cup ground flax seeds, and the remaining 1/2 teaspoon sea salt.
Pour the peanut butter–honey mixture over the dry ingredients and mix until evenly combined. If the mixture is warm, cover and chill in the refrigerator about 15 minutes to firm up.
Fold 3 ounces of the chopped dark chocolate into the cooled mixture. Reserve the remaining 3 ounces for topping.
Scoop about 1 1/2 to 2 tablespoons of mixture for each bite, roll into balls, then flatten each ball into a disk about 1/2 inch thick. Place the disks on the prepared second baking sheet.
Sprinkle a little of the roasted coffee (from the coated almonds) over the bites if desired. Press 3–4 of the cooled roasted almonds into the top of each bite.
Place the remaining 3 ounces chopped dark chocolate in a microwave-safe bowl. Melt in 30-second intervals, stirring after each, until smooth (about 1 minute total). Drizzle the melted chocolate over the almonds on each bite; sprinkle a bit more roasted coffee on top if desired.
Put the baking sheet in the freezer for 5–10 minutes to harden the chocolate. Transfer the bites to an airtight container and store at room temperature or in the refrigerator.