Preheat the oven to 350°F (175°C). Line two baking sheets with parchment paper or nonstick baking mats; set aside.

In a medium bowl, whisk together 1½ cups whole wheat pastry flour, 1½ cups old fashioned rolled oats, ½ teaspoon baking soda, and ½ teaspoon salt until evenly combined.

In a large bowl, use an electric mixer on medium speed to cream ¾ cup (1½ sticks) unsalted butter (at room temperature), ½ cup granulated white sugar, and 1 cup packed brown sugar until light and fluffy, about 1–2 minutes.

Add 1 cup creamy peanut butter to the creamed sugars and butter and mix on medium until incorporated, about 30 seconds.

Add the 2 large eggs and 1 teaspoon vanilla extract to the bowl and mix on medium until the mixture is smooth and homogeneous, scraping down the sides of the bowl as needed.

With the mixer on low speed, add the dry flour-oat mixture to the wet ingredients in about two additions. After the dry ingredients are mostly incorporated, increase speed to medium and beat just until well blended; do not overmix.

Stir in ¾ cup milk chocolate or semi-sweet chocolate chips and ¾ cup broken stick pretzels by hand with a spatula until evenly distributed.

Using an ice cream scoop or a large spoon, portion the dough into 12 equal mounds on each prepared baking sheet (24 total), spacing them about 2 inches apart.

Dip the bottom of a glass in water, then gently press each mound to flatten slightly. If desired, press a few extra chocolate chips and pretzel pieces onto the top of each cookie for a decorative finish.

Bake one sheet at a time on the middle oven rack until the cookies are nicely browned around the edges, about 14 minutes.

Let the cookies cool on the baking sheet for a few minutes (2–5 minutes), then transfer them to a wire rack to cool completely.