These Morning Glory Muffins are the kind of recipe I reach for when I need something dependable, not fussy, and genuinely satisfying for breakfast or an on-the-go snack. They carry the warmth of grated carrots and apple, a bit of spice, toasted nuts, and a sweet-tart hit from dried cranberries. The surprise is the soft cream cheese center that keeps each bite moist and just a touch indulgent.

I test recipes so you won’t have to guess. This version is built around a specific method and ingredient list; follow it and you’ll get consistent results. I’ll walk you through what matters most — from the exact assembly order and the one-minute cream cheese step, to how to store and reheat these for the week.

No fluff, just practical tips and clear steps. If you like muffins that are tender, not too sweet, and have texture and character, these Morning Glory Muffins are worth the prep. Read on, then bake a batch.

Ingredients at a Glance

6 ounces (170 grams) cream cheese, room temperature — makes the creamy center; soften to avoid lumps.
2 tablespoons (24 grams) granulated sugar — sweetens the cream cheese filling.
2 tablespoons (16 grams) all-purpose flour — stabilizes the filling so it holds shape.
1½ tablespoons (22.5 grams) whole milk — loosens the filling for piping.
½ teaspoon (3 grams) vanilla bean paste — flavor boost for the filling.
½ cup (110 grams) firmly packed light brown sugar — adds moistness and depth to the batter.
½ cup (112 grams) canola oil — keeps muffins tender; neutral-flavored.
¼ cup (50 grams) granulated sugar — balances sweetness and structure in the batter.
¼ cup (60 grams) whole milk, room temperature — hydrates the batter and helps dissolve sugars.
2 large eggs (100 grams), room temperature — provides lift and structure.
1 large egg yolk (19 grams), room temperature — adds richness.
½ teaspoon (3 grams) vanilla bean paste* — general batter flavoring.
1¼ cups (135 grams) grated peeled carrots (about 3 large carrots) — primary moist element and texture.
½ cup (83 grams) grated peeled Golden Delicious apple — adds natural sweetness and moisture.
1 cup (125 grams) all-purpose flour — main structure.
?cup (87 grams) whole wheat flour — adds nuttiness and a bit of chew (measure shown as provided).
1 tablespoon (6 grams) pumpkin pie spice — warm spice blend; key flavor driver.
1½ teaspoons (7.5 grams) baking soda — leavening for tender rise.
1¼ teaspoons (3.75 grams) kosher salt — balances sweetness and enhances flavor.
?cup (43 grams) dried sweetened cranberries, roughly chopped — bright, chewy contrast (measure shown as provided).
½ cup (57 grams) finely chopped toasted pecans — crunch and toasty flavor; toast for best results.

Morning Glory Muffins: How It’s Done

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.

The Upside of Morning Glory Muffins

These muffins hit a few practical sweet spots: they’re portable, they keep well for a few days, and they combine fruit, vegetable, nuts, and a touch of indulgence in one bite. The grated carrot and apple mean you get moisture and texture without a heavy batter. Toasted pecans add crunch that contrasts nicely with the soft cream cheese center.

The method is forgiving. You mix wet and dry separately, fold just until combined, and bake immediately. That means you won’t overwork the batter and end up with tough muffins. The cream cheese center looks and tastes like extra effort, but it’s quick — a one-minute beat and a few squeezes from a pastry bag.

What to Use Instead

Need to swap something? Keep these practical notes in mind.

Neutral oil: canola oil keeps the flavor neutral. Use another neutral oil (vegetable or light olive oil) if you prefer. For a slight flavor change, melted unsalted butter will work but may tighten crumb slightly.

Milk: whole milk is listed. You can use 2% or a plain unsweetened plant milk (like oat or almond) in the batter — they hydrate the batter similarly. If you use a thinner plant milk, the batter may be a touch looser; proceed carefully.

Whole wheat flour: the recipe includes a portion of whole wheat. If you don’t have it, you can use the same weight in all-purpose flour for a milder flavor and lighter texture. For a heartier result, use a whole-grain flour you like, but expect a denser crumb.

Nuts and fruit: toasted pecans add flavor; swap with toasted walnuts or almonds if that’s what you have. Dried cranberries can be replaced with raisins, chopped dried cherries, or dried apricots — keep the same approximate volume but chop larger dried fruit into small pieces.

Cream cheese filling: if you prefer no filling, skip it and bake longer until centers are set, watching carefully so they don’t dry out. Or replace the cream cheese with a thick nut butter for a different profile, keeping the same idea for piping or spooning a small amount into each cup.

Must-Have Equipment

12-well muffin pan — the recipe is scaled for one standard pan.
Baking spray with flour or grease and flour — ensures easy removal and intact bottoms.
Stand mixer with paddle attachment — speeds up cream cheese filling prep and gives a smooth texture.
Pastry bag (or resealable bag) — for piping the cream cheese center neatly; cut a ½-inch hole if you don’t have a tip.
Box grater or food processor — for quick, consistent grating of carrots and apple.
Wire rack — cools muffins evenly to preserve texture.

Don’t Do This

Do not overmix the batter. Stir until the dry ingredients are moistened and stop; overworking creates tunnelled, dense muffins. Do not skip toasting the pecans — raw nuts are softer and less flavorful. Don’t pipe the cream cheese to touch the bottom of the cup; that will create a pocket that leaks or bakes oddly. And don’t overbake: check with a skewer avoiding the cream cheese center.

Holiday-Friendly Variations

These muffins adapt well to seasonal tweaks. For autumn or winter, increase the warm spice profile by adding a pinch more pumpkin pie spice or a sprinkle of ground nutmeg on top before baking. For spring, swap the dried cranberries for chopped dried apricots and add a tablespoon of orange zest to the batter for brightness. Top with a light maple glaze for holiday brunches, or fold in a handful of shredded coconut for a tropical touch.

Notes from the Test Kitchen

Texture and timing matter. The batter should be thick but spoonable; it won’t pour. If your grated apple is very wet, press it lightly in a towel — you want the moisture, not puddles. The cream cheese filling should be smooth and easy to pipe; any lumps mean the cream cheese wasn’t softened enough.

Oven temperatures vary. I recommend checking the muffins at 11 minutes if your oven runs hot; the range given (12–14 minutes) is the typical window. A wooden pick inserted into the muffin outside the cream cheese center should come out with a few moist crumbs.

When piping, insert the tip into the batter and apply gentle, steady pressure. If you notice filling seeping or the batter collapsing, you may have overfilled the cups; reduce the filling slightly next time.

Save for Later: Storage Tips

Short-term (1–3 days)

Cool muffins completely on a wire rack. Store in an airtight container at room temperature for up to 2 days. Because of the cream cheese center, refrigeration is recommended if you plan to keep them longer.

Long-term (up to 3 months)

For longer storage, freeze cooled muffins in a single layer on a baking sheet until firm, then transfer to a labeled freezer bag or airtight container. Press a piece of parchment between layers to prevent sticking. Thaw overnight in the refrigerator or on the counter for a couple hours. Reheat briefly in a 325°F (160°C) oven for 8–10 minutes or microwave for 20–30 seconds to refresh warmth.

Common Questions

Can I make mini muffins? Yes. Reduce baking time and check frequently; start checking at 8 minutes. Fill mini cups about 3/4 full and be gentle with the cream cheese filling to avoid overflow.

Why toast the pecans? Toasting intensifies flavor and gives a crunch that stands up to the soft muffin crumb. Toast on a baking sheet at 350°F for 6–8 minutes or in a dry skillet until fragrant.

Can I skip the cream cheese filling? You can omit it, but the muffins will be less moist and miss the creamy center contrast. If you skip it, bake until a skewer inserted into the center comes out clean, and expect a slightly longer bake time.

Do I have to use Golden Delicious apple? No — any firm, sweet-tart apple will work. Golden Delicious yields a mild sweetness and tender texture, but Granny Smith, Fuji, or Honeycrisp are fine alternatives.

Bring It Home

If you follow the ingredients and the steps above, you’ll have a reliable batch of Morning Glory Muffins that balance wholesome components with a touch of indulgence. They’re great to make ahead for the week, freeze for later, or share at a neighborly breakfast. Bake a batch, take note of how your oven behaves, and tweak small elements (nuts, dried fruit, or a splash of citrus) to make them yours.

Leave a note about how yours turned out — I love hearing what substitutions or variations readers try. Happy baking.

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Morning Glory Muffins

Moist carrot-and-apple muffins filled with a sweet cream cheese center and studded with dried cranberries and toasted pecans.

Prep Time40

Cook Time44

Total Time1 54

Course: Breakfast

Servings: 4 servings

Ingredients

6 ounces 170 grams cream cheese, room temperature
2 tablespoons 24 grams granulated sugar
2 tablespoons 16 grams all-purpose flour
1 1/2 tablespoons 22.5 grams whole milk
1/2 teaspoon 3 grams vanilla bean paste
1/2 cup 110 grams firmly packed light brown sugar
1/2 cup 112 grams canola oil
1/4 cup 50 grams granulated sugar
1/4 cup 60 grams whole milk, room temperature
2 large eggs 100 grams, room temperature
1 large egg yolk 19 grams, room temperature
1/2 teaspoon 3 grams vanilla bean paste*
1 1/4 cups 135 grams grated peeled carrots (about 3 large carrots)
1/2 cup 83 grams grated peeled Golden Delicious apple
1 cup 125 grams all-purpose flour
?cup 87 grams whole wheat flour
1 tablespoon 6 grams pumpkin pie spice
1 1/2 teaspoons 7.5 grams baking soda
1 1/4 teaspoons 3.75 grams kosher salt
?cup 43 grams dried sweetened cranberries, roughly chopped
1/2 cup 57 grams finely chopped toasted pecans

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.

Equipment

Oven
12-well muffin pan
baking spray or grease and flour
stand mixer with paddle attachment
Medium Bowl
Large Bowl
Whisk
pastry bag and 1/2-inch round piping tip (or 1/2-inch opening)
Wire Rack
wooden pick or toothpick

Notes

Notes
*
We used Heilala Pure Vanilla Bean Paste.
We used a Williams Sonoma Goldtouch Pro Muffin Pan.