Preheat the oven to 350 degrees F. Line a 12-cup muffin pan with paper liners. Whisk both flours, the baking powder and salt in a large bowl. Whisk 1/3 cup peanut butter, the milk, brown sugar, melted butter, vanilla and eggs in a medium bowl; stir into the flour mixture until just combined.
Divide the batter among the muffin cups, filling them three-quarters of the way. Tap the bottom of the pan lightly on the counter to smooth out the batter. Bake until the muffins are lightly browned and a toothpick inserted into the center comes out clean, about 25 minutes. Let the muffins cool 5 minutes in the pan, then remove to a rack to cool completely.
Using a melon baller or teaspoon, scoop out a shallow hole in the middle of each muffin. Melt the remaining 2/3 cup peanut butter in the microwave until loose, stirring halfway through, 45 to 60 seconds. Spread the peanuts on a plate. Dip the top of 1 muffin in the melted peanut butter, letting the excess drip off, then dip it in the chopped peanuts to coat. Transfer to the rack and repeat with the remaining muffins.
Spoon 1 heaping tablespoon jelly or jam into the hole in each muffin. Let set 5 minutes.