Preheat an oven to 180c (350f) and prep a 12-cup muffin pan with paper liners. Peel and cut the stems of the carrot and grate them on the small or medium grater. Peel and core a large apple and grate it the same way.
Into a large mixing bowl, add the grated carrots, grated apple, vanilla extract, cinnamon, eggs, brown sugar, nutmeg, vegetable oil, ginger, kosher salt, honey, chopped pecans, and orange juice.
Mix the batter using a wooden spatula or a rubber spatula until the ingredients are well combined.
Add the whole wheat flour and baking soda and mix until just combined and there are no lumps of flour visible. Do not overmix the batter to ensure that your muffins are moist and tender.
Let the batter sit at room temperature for at least 30 minutes. This step creates the signature domed tops that the best muffins have!
Scoop the batter with a large ice cream scooper into the muffin tins, filling them almost completely. You should have about 14-16 muffins, you can bake them in two batches.
Bake in a 200c (400f) preheated oven for 5 minutes, and then bake for another 12-14 minutes at 180c (350f) or until a toothpick comes out clean.
Let the muffins cool for at least 20 minutes before eating. Serve and enjoy!