Step 1

Place a rack in middle of oven; preheat to 350°. Lightly coat flat top of a standard 12-cup muffin pan with nonstick spray (this will prevent muffins from gluing themselves to the pan). Line cups with double layers of muffin liners. Cut apples into quarters; remove cores. Cut each quarter into 4 wedges; set aside.

Step 2

Pulse pecans in a food processor until you have a fine meal with a bit of texture, like coarse sand. Heat a large skillet over medium-high, then add pecans and toast, stirring, until darkened and very fragrant (it’s okay if they’re even a tiny bit burnt in spots), about 3 minutes. Transfer to a large bowl and let cool slightly.

Step 3

Wipe out skillet and return to medium-high heat. Melt butter, swirling pan so that it’s evenly coated, until foaming, then add reserved apples. Drizzle with honey and generously sprinkle with sea salt. Cook, tossing often, until apples are tender and deep golden brown and glazed with honey, about 5 minutes. Scrape into a medium bowl and let cool.

Step 4

Add all-purpose flour, spelt flour, baking powder, baking soda, and kosher salt to nuts; whisk to combine. Beat eggs and granulated sugar in the bowl of a stand mixer fitted with the whisk attachment on high speed until mixture is thick, pale, and tripled in volume, 8–10 minutes.

Step 5

Combine oil and buttermilk in a measuring glass. With motor running, gradually pour into egg mixture, stopping as soon as incorporated to prevent eggs from deflating. Scrape into bowl with dry ingredients and fold until just combined (be careful not to overmix). Scoop about 2 Tbsp. batter into each muffin cup and place an apple slice on top. Divide remaining batter among muffin cups, filling until just below the top (you may have a spoonful or two of batter left over). Place 1 apple slice on top of each, then spoon any glaze left in the bowl on top. (You’ll have a few leftover apple slices; eat them.) Sprinkle each muffin with some raw sugar and a pinch of sea salt.

Step 6

Bake muffins until golden brown all over, rotating pan halfway through, 22–28 minutes. Let cool in pan 10 minutes, then transfer to a wire rack and let cool completely.

Step 7

Do Ahead: Batter can be made 2 days ahead. Cover and chill.