Position a rack in the center of the oven and preheat to 350°F. Line an 8×8‑inch baking pan with parchment leaving a 1‑inch overhang on two sides so you can lift the cake out easily; lightly grease the parchment.
Toast the pecans in a dry skillet over medium heat, stirring, until fragrant and slightly darkened (about 3 minutes). Remove to a small plate to cool, then roughly chop.
In a medium bowl whisk together oat flour, almond flour, pumpkin pie spice, baking soda, and salt until evenly blended.
In a large bowl combine the pumpkin puree, coconut sugar, Greek yogurt, eggs, and vanilla. Whisk until the mixture is smooth and the sugar begins to dissolve, about 30 seconds.
Pour the dry ingredients into the wet mixture and fold with a spatula just until no streaks of flour remain—do not overmix. Fold in the chopped toasted pecans, reserving a few for the top.
Scrape the batter into the prepared pan, smooth the surface, and scatter the reserved pecans on top. Bake for 32–38 minutes, rotating once halfway through, until the top is set and a toothpick inserted into the center comes out with a few moist crumbs.
Allow the cake to cool in the pan on a wire rack for about 25 minutes, then use the parchment overhang to lift it out and cool completely on the rack (at least another 30 minutes) before frosting.
For the frosting, beat together the softened cream cheese, Greek yogurt and powdered sugar until smooth and spreadable. If you prefer a lighter glaze, whisk the ingredients until slightly thinner by adding a teaspoon of milk at a time.
Spread the frosting over the fully cooled cake, slice into 16 pieces, and serve. Store leftovers covered in the refrigerator for up to 4 days.