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Line an 8x8-inch baking pan with parchment paper, leaving some overhang on the sides for easy removal.
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In a large mixing bowl, stir together the peanut butter, maple syrup, and vanilla extract until smooth and well combined.
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Add the protein powder, almond flour, and salt. Mix until a thick, uniform dough forms with no dry spots remaining.
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Transfer the mixture to the prepared pan and use the back of a spoon, an offset spatula, or your hands to press it into an even layer.
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In a microwave-safe bowl, combine the chocolate chips and coconut oil. Microwave in 20-second intervals, stirring between each, until the chocolate is completely melted and smooth.
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Pour the melted chocolate over the peanut butter layer and spread it evenly to the edges with an offset spatula or the back of a spoon. Sprinkle with flaky sea salt, if desired.
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Transfer the pan to the freezer for 30–60 minutes, or until the chocolate is completely set and the bars are firm.
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Lift the bars out of the pan using the parchment paper and slice into squares or rectangles. Enjoy immediately, or store for later.