Instructions

• Preheat oven to 375°F (190°C). Position a rack in the center of the oven. Spray a 12-well muffin pan with baking spray that contains flour or grease and flour the wells.
• Make the cream cheese filling: in the bowl of a stand mixer fitted with the paddle attachment, beat 6 ounces (170 g) cream cheese at medium speed until smooth and creamy, about 1 minute, stopping once to scrape down the sides.
• Add 2 tablespoons (24 g) granulated sugar, 2 tablespoons (16 g) all-purpose flour, 1½ tablespoons (22.5 g) whole milk, and ½ teaspoon (3 g) vanilla bean paste to the cream cheese. Beat at medium speed until smooth and well combined. Transfer the filling to a pastry bag and cut a ½-inch opening in the tip (or fit a ½-inch round piping tip). Set the filled pastry bag aside.
• In a medium bowl, whisk together ½ cup (110 g) light brown sugar, ½ cup (112 g) canola oil, ¼ cup (50 g) granulated sugar, ¼ cup (60 g) whole milk (room temperature), 2 large eggs (100 g), 1 large egg yolk (19 g), and ½ teaspoon (3 g) vanilla bean paste until smooth.
• Stir the grated ingredients into the wet mixture: add 1¼ cups (135 g) grated peeled carrots and ½ cup (83 g) grated peeled Golden Delicious apple and whisk until evenly distributed.
• In a large bowl, whisk together the dry ingredients: 1 cup (125 g) all-purpose flour, 87 g whole wheat flour, 1 tablespoon (6 g) pumpkin pie spice, 1½ teaspoons (7.5 g) baking soda, and 1¼ teaspoons (3.75 g) kosher salt.
• Add the wet carrot-apple mixture to the dry ingredients and stir gently just until the dry ingredients are moistened and no large pockets of flour remain. Do not overmix.
• Add 43 g dried sweetened cranberries (roughly chopped) and ½ cup (57 g) finely chopped toasted pecans to the batter and fold until just combined.
• Divide the batter among the prepared muffin wells, filling each cup about 3/4 full (leave about 1/4 inch [6 mm] space below the rim of each well).
• Pipe the cream cheese filling into the center of each muffin: insert the tip into the batter without touching the bottom or sides and pipe an even amount of filling into each cup so the filling sits in the center. Use the tip or the back of a spoon to pull a small amount of filling into the top of the batter and create a slight swirl if desired. Do not overfill.
• Bake on the center rack until the muffin tops are set and a wooden pick inserted into the muffin (avoiding the cream cheese center) comes out with only a few moist crumbs, about 12 to 14 minutes.
• Let the muffins cool in the pan for 5 minutes, then remove them from the pan and transfer to a wire rack. Serve warm or let cool completely.