Heat the oven to 350°F. Line a 12-cup muffin tin with paper liners or spray each cup lightly with oil.
Shred the zucchini with the large holes of a box grater. Gather the shreds in a clean kitchen towel, squeeze firmly over the sink until most moisture is removed, then set the squeezed zucchini aside.
In a medium bowl whisk together the peanut butter, agave nectar, eggs, and vanilla until smooth and glossy. A fork or small whisk works well — you want a homogenous wet base.
In a separate larger bowl stir the almond flour, baking powder, and sea salt to distribute the leavening evenly through the dry mix.
Pour the wet mixture into the dry ingredients and fold with a spatula until mostly combined. Let the batter rest 8–10 minutes so the almond flour hydrates and the batter firms slightly.
Gently fold the squeezed zucchini and half of the chocolate chips into the rested batter until evenly distributed. Reserve the remaining chips for topping.
Spoon the batter into the prepared muffin cups, filling each about three-quarters full. Sprinkle the remaining chocolate chips over the tops and gently tap the pan on the counter to remove air pockets and level the batter.
Bake in the preheated oven for 18–22 minutes, rotating the pan once halfway through, until the tops are set and a toothpick inserted near the center comes out with only a few moist crumbs.
Allow the muffins to cool in the tin for 8–10 minutes, then transfer them to a wire rack to cool completely. Cooling helps them firm up and improves texture.