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For the cookies:.
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Preheat oven to 350.
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Line two baking sheets with Silpats.
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In a small bowl, mix baking soda, salt and flour.
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In the bowl of an electric mixture, beat butter and peanut butter until smooth.
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Add brown sugar, and beat until lightened and combined, about 2 minutes.
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Add eggs one at a time, beating after each addition until incorporated.
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Add vanilla.
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Add ingredients to the batter all at once, mixing slowly until just combined.
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The mixture will look very wet and oily; this is OK.
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Roll dough into balls about 3/4-1 inch in diameter, and space about 1 1/2 inches apart on each cookie sheet.
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Bake until lightly golden and dry on top, about 12 minutes.
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Remove from oven, let rest for 5 minutes, and transfer to a wire rack to cool.
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For the ganache:.
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Meanwhile, make the ganache.
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Put chopped chocolate into a small, heatproof bowl.
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In a small saucepan, heat cream until just boiling, then pour over chopped chocolate.
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Mix well until smooth and fully incorporated.
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Chill until the chocolate mixture reads 70 degrees on a thermometer.
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This will be the best spreading consistency.
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To assemble:.
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Spread about 1 rounded teaspoon of the ganache on the flat side of a cookie with a small offset spatula.
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Top with a second cookie, flat side on the filling, forming sandwich.
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Repeat with remaining filling and cookies.