Toast pepitas in a dry skillet over medium heat. Set aside and allow to cool.
Heat oven to 350°F. Line baking sheets with parchment paper; set aside.
In a large bowl, whisk together flour, cocoa powder, salt, baking soda, and spices.
In the bowl of a stand mixer fitted with paddle attachment, beat butter and sugars on medium-high until light and fluffy.
Add eggs one at a time, mixing until thoroughly combined. Mix in vanilla.
Add 1/3 of the flour mixture to butter mixture, mixing on low until it’s almost all incorporated. Scrape down bowl. Repeat two more times with rest of flour mixture.
Reserve a wee bit of pumpkin seeds and chocolate chips. Fold in remaining pepitas, chocolate chips, and dried cranberries.
Form dough into balls that are about 1 ½ tablespoons each. (A #40 cookie scoop is super helpful here.) Top each with a couple chocolate chips, a couple pepitas, and sprinkling of flaky sea salt.
Bake for 10–12 minutes or until edges are set.
Let cookies cool on baking sheets for about 10 minutes before transferring cookies to wire rack to cool completely.
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