Slice about half an inch off the stem end of the onion to create a flat surface. Leave the root end completely intact — this holds the petals together. Peel away all the papery outer skin.
Place the onion cut-side down with the root pointing up. Starting half an inch from the root, make a firm downward cut to the board. Rotate and repeat to divide the onion into 4 quarters. Make 2–3 additional cuts within each quarter for roughly 16 petal sections. Do not cut through the root.
Flip the onion over so it rests on its root. Let it sit for 5 minutes to allow the petals to naturally fan out. Gently pry the petals apart with your fingers.
In a wide shallow bowl, whisk together the whole wheat flour, smoked paprika, garlic powder, cayenne pepper, thyme, and oregano until evenly blended. In a second bowl, vigorously whisk the eggs and almond milk until combined.
Place the onion cut-side up in a large mixing bowl. Spoon the seasoned flour mixture generously over the entire onion, working it into every crevice. Pick up the onion and tap off any excess flour.
Lower the floured onion into the egg wash, coating all petals thoroughly. Lift it out and let the excess liquid drip away. Return the onion to the seasoned flour bowl for a second coating. Shake off excess flour.
Place the breaded onion in the refrigerator and chill for 10 minutes. This allows the coating to hydrate and bond so it stays crispy during cooking.
Preheat your air fryer to 350°F (175°C) for at least 3 minutes. Fold a long piece of aluminum foil into a sturdy sling for easy handling.
Remove the onion from the fridge. Generously spray the entire onion — including deep inside the petals — with olive oil or avocado oil spray.
Lower the onion cut-side up into the air fryer basket using the foil sling. Cook for 25 minutes, spraying any dry white flour spots with oil 2–3 times during cooking. The onion is done when it is deeply golden and crispy all over.
Carefully lift the onion out using the foil sling and transfer to a serving platter. Season with sea salt and freshly ground black pepper. Serve immediately with spicy mayonnaise, tangy barbecue sauce, or garlic yogurt.