Heat the oven to 425°F (218°C) and prepare a 12-count muffin pan with nonstick spray or greased/sprayed cupcake liners, then ready a second pan or plan to bake in batches since the batter makes 14–16 muffins. The batter volume is generous, so having space ready from the start keeps the process smooth.

Whisk the flour, baking soda, cinnamon, ginger, salt, and flaxseed in a large bowl until evenly combined. This distributes the leavening and spices well, which helps the muffins rise evenly and prevents stray green spots from poorly mixed baking soda.

In a separate medium bowl, whisk the eggs, brown sugar, honey, oil, applesauce, orange zest, orange juice or pineapple juice, and vanilla until the mixture looks blended and smooth. You should see an even, glossy mixture with no streaks of egg left behind.

Whisk the carrots and apple into the wet mixture, then add the wet ingredients to the dry bowl and stir briefly with a wooden spoon or silicone spatula before folding in the raisins and pecans. The batter will look very thick and chunky, and that’s exactly what you want for a hearty muffin.

Fold just until no dry flour pockets remain, then divide the batter into the liners and fill them all the way to the top. Stop mixing as soon as the batter comes together so the finished muffins stay tender instead of tough.

Bake for 5 minutes at 425°F (218°C), then lower the oven temperature to 350°F (177°C) without opening the oven door and continue baking for 18 minutes more. The tops should rise high and smell warmly spiced, with cinnamon and ginger especially noticeable near the end.

Check the center with a toothpick, then cool the muffins in the pan for 10 minutes before moving them to a wire rack. If the toothpick comes out clean, the crumb is set and the muffins are ready to finish cooling.