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In a medium bowl, combine the peanut butter, maple syrup, vanilla extract, almond flour, and sea salt. Mix until a dough forms. Set aside while you prepare the chocolate.
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Add the dark chocolate and coconut oil to a small saucepan. Heat over low heat, stirring frequently, until completely melted and smooth.
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Place your silicone peanut butter cup mold on a small baking sheet or plate for easy transfer. Add about 1 teaspoon of melted chocolate to the bottom of each cavity. Gently tap the mold on the counter to spread the chocolate evenly.
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Transfer the mold to the freezer and freeze for about 30 minutes, or until the chocolate layer is completely set.
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Remove the mold from the freezer. Add about 7–8 grams of peanut butter filling to each cup and gently press it into an even layer, leaving a little room around the edges for the top chocolate layer.
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Spoon about 1 teaspoon of melted chocolate over each peanut butter center. If you have any chocolate remaining, divide it evenly among the cups to fill them closer to the top. Sprinkle with flaky sea salt, if desired.
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Return the mold to the freezer and freeze for at least 1 hour, or until the peanut butter cups are completely firm.
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Carefully remove the peanut butter cups from the mold and enjoy straight from the refrigerator or freezer.
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Storage: Store the peanut butter cups in an airtight container in the refrigerator for up to 1 week.
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For longer storage, keep them in the freezer for up to 3 months. If frozen, allow them to sit at room temperature for a few minutes before enjoying for the best texture.