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Preheat the oven to 350F. Grease and line a 9in x 9in pan with parchment paper (you could use an 8in x 8in pan as well, but the brownies will be thicker).
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Pulse the almonds in a food processor for 5-10 seconds intervals. About 10 pulses should get the almonds finely ground. Transfer to a large mixing bowl.
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Sift the flour, arrowroot, cocoa, salt and baking soda into the same mixing bowl as the almonds. Whisk well to combine, set aside.
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In a small bowl combine the flax and water, set aside.
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Place the vegan butter in a microwave safe container and microwave at half power for 30 seconds (you can also melt the butter on the stove if you don't have a microwave). Add the 3/4 cup chocolate chips and continue to microwave at half power for 30 second intervals, stirring in between each, until the chocolate is completely melted.
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Stir the sugar into the melted chocolate mixture, followed by the rice milk, vanilla and flax. Whisk well to combine.
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Pour the chocolate mixture into the bowl with the dry ingredients and mix well to combine. The batter will be very thick.
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Fold in the optional chocolate chips and then spoon into the prepared pan. Use a spatula to spread evenly, you can also wet your hands and press the batter into the pan to smooth it out.
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Bake at 350 for about 35 minutes or until a toothpick comes out somewhat clean.
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Let cool for at least 2 hours before cutting.