Preheat the oven to 350 degrees F (180 C). Line a 9x9-inch square baking pan with parchment paper, or coat lightly with non-stick cooking spray.
In a large bowl, combine the oats, flour, brown sugar, baking powder, salt, cinnamon, nutmeg, and flaxseed, if using; stir briefly to blend.
In a separate medium bowl, combine the peanut butter, pumpkin, eggs, honey, milk, and vanilla extract; whisk until smooth.
Pour the pumpkin mixture into the bowl with the dry ingredients, and stir just until evenly combined; do not overmix. Add chocolate chips, and fold gently to combine.
Press the mixture into the prepared pan, and sprinkle additional chocolate chips on top, if desired. Bake for 20-25 minutes, until the middle is set and the top is lightly browned. Remove to a wire rack and let cool to room temperature before slicing into bars.
Serve at room temperature, or warmed for 10 seconds in the microwave. Bars can be stored at room temperature for 2-3 days, in the fridge for up to 1 week, or in the freezer for 2-3 months.