Name: Chocolate Chip Whole Wheat Muffins Recipe
Prep time: 14 min
Cook time: 18 min
Total time: 32 min
Cuisine: American
Ingredients: 1 ¾ cups whole wheat pastry flour or white whole wheat flour or regular whole wheat flour or all-purpose flour (215 grams); 1 teaspoon baking powder; ½ teaspoon baking soda; ½ teaspoon fine salt; 1 teaspoon ground cinnamon; ⅓ cup melted coconut oil or extra-virgin olive oil; ½ cup runny honey; 2 eggs, preferably at room temperature; 1 cup plain Greek yogurt; 2 teaspoons vanilla extract; 1 cup chocolate chips (semi-sweet to dark); Optional: 1 tablespoon turbinado sugar (raw sugar), for sprinkling on top

There’s something so comforting about fresh-from-the-oven muffins, right? This Chocolate Chip Whole Wheat Muffins Recipe blends wholesome whole wheat goodness with melty chocolate chips, creating a perfect balance of healthy and indulgent that I can never resist.

Two pieces of a chocolate chip muffin are shown on a white plate with scalloped edges. Each muffin piece reveals a soft, light golden interior with dark, melted chocolate chips scattered inside. The muffin's texture looks moist and crumbly with slightly crispy edges on top. The plate sits on a white marbled surface with a blue woven cloth partially visible at the bottom left corner and a few loose chocolate chips nearby. photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Chocolate Chip Whole Wheat Muffins Recipe
Top Tip
How to Serve Chocolate Chip Whole Wheat Muffins Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Chocolate Chip Whole Wheat Muffins Recipe

Why You'll Love This Recipe

I got hooked on this recipe because it’s easy to make yet feels like a little morning celebration. Plus, these muffins manage to be moist, tender, and packed with flavor — all without relying on all-purpose flour alone.

Whole Wheat but Tender: Using whole wheat pastry flour keeps the muffins hearty but still soft and light.
Natural Sweetness: Honey adds gentle sweetness and moisture, keeping things wholesome.
Chocolate Chip Perfection: Tossing the chips with cinnamon before folding helps them disperse evenly and never sink.
Simple Ingredients: Stuff you probably have in your pantry — no fancy items to hunt down.

Ingredients & Why They Work

Each ingredient in this Chocolate Chip Whole Wheat Muffins Recipe plays a role in the texture and flavor, making sure these muffins come out just right. Let me walk you through why they matter and how to get the best results.

Flat lay of a mound of whole wheat flour on a simple white ceramic plate, a small white bowl filled with semi-sweet chocolate chips dusted with ground cinnamon, two whole uncracked brown eggs, a small white bowl of golden runny honey, a small white bowl with melted coconut oil, a small white bowl with thick plain Greek yogurt, and a small white ceramic bowl holding a light beige powder of baking powder and baking soda mixed together, all arranged with perfect symmetry, placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Whole wheat pastry flour: This flour is lighter than regular whole wheat, which means the muffins won’t be too dense but still have that nutty flavor we love.
Baking powder & baking soda: These are your leavening agents to help the muffins rise beautifully and stay light.
Fine salt: Enhances all the other flavors—don’t skip it!
Melted coconut oil or olive oil: Adds moisture and richness. Coconut oil gives a subtle tropical hint, but olive oil keeps the flavor neutral.
Honey: Keeps the muffins naturally sweet and tender, plus it gives them a lovely golden color.
Eggs: Provide structure and richness. Using room-temperature eggs helps them combine more smoothly.
Plain Greek yogurt: This is the secret weapon for moist, tender crumb. I’ve tried different fat percentages, and all work well, but I prefer whole milk Greek yogurt for extra richness.
Vanilla extract: Just the right touch to boost the chocolate and honey flavors.
Chocolate chips: Semi-sweet or dark are my favorites—they melt just enough and balance the sweetness.
Ground cinnamon: Mixed with the chocolate chips, this little spice keeps the chips from sinking and adds warmth.
Turbinado sugar (optional): Sprinkled on top, this gives the muffins a slight crunch and sparkle, which looks so inviting.

Note: Exact ingredients and measurements are listed in the recipe card below.

Make It Your Way

I love playing around with this Chocolate Chip Whole Wheat Muffins Recipe to keep things interesting, and you should too! Whether it’s swapping in alternative chips or tweaking for dietary needs, this recipe is a dream for personal touches.

Vegan Version: I’ve replaced eggs with flax eggs and swapped yogurt for vegan yogurt or homemade buttermilk—it works surprisingly well to keep that tender texture.
Gluten-Free: I use Bob’s Red Mill gluten-free flour blend sometimes, and the muffins still come out great, though a bit denser.
Flavor Twists: Try white chocolate chips or add a handful of chopped nuts or dried fruit for extra texture and color.

Step-by-Step: How I Make Chocolate Chip Whole Wheat Muffins Recipe

A clear glass bowl filled with thick, creamy batter that is light beige in color with small dark brown chunks spread throughout. The batter has a slightly lumpy, soft texture with uneven swirls and some streaks of a darker shade. A shiny silver spoon with a patterned handle rests inside the bowl, partially submerged in the batter. The bowl sits on a white marbled surface. photo taken with an iphone --ar 2:3 --v 7

Step 1: Prep Your Oven and Muffin Tin

Start by preheating your oven to 375°F (190°C). Line a 12-cup muffin tin with liners or lightly grease each cup with butter, coconut oil, or cooking spray. I like to use liners for easy clean-up, but greasing works just as well—trust me, these muffins won’t stick.

Step 2: Combine the Dry Ingredients

In a large bowl, whisk together the whole wheat pastry flour, baking powder, baking soda, fine salt, and cinnamon. Making sure these are evenly mixed helps your muffins rise evenly and develop great flavor.

Step 3: Mix the Wet Ingredients

In another bowl, whisk the melted coconut oil and honey together until smooth. Add the eggs and beat well, then stir in the Greek yogurt and vanilla extract. If your coconut oil hardens because the yogurt is cold, heat the mixture gently in 30-second bursts in the microwave until combined.

Step 4: Bring It Together

Pour the wet mixture into the dry ingredients. Use a big spoon or spatula to gently fold until just combined—you should still see a few lumps. Overmixing will make your muffins tough, so stop as soon as the flour is mostly absorbed.

Step 5: Add Chocolate Chips

Toss the chocolate chips with the ground cinnamon in a small bowl. This step is key to keep the chips evenly spread so they don’t all sink to the bottom during baking. Fold the chocolate chip mixture into the batter gently.

Step 6: Fill and Bake

Divide the batter evenly into your muffin cups—don’t worry if they’re full, that’s perfect for a nice dome. If you want, sprinkle the tops with raw turbinado sugar for a little crunchy sparkle. Bake for 16-18 minutes until golden on top and a toothpick inserted into the center comes out clean, though it’s okay if it has streaks of melted chocolate.

Step 7: Cool and Enjoy

Place your muffin tin on a cooling rack to let the muffins cool a bit before removing. These are perfect warm but also taste great at room temperature.

Top Tip

Through making this recipe a few times, I’ve picked up some tricks that really make a difference in your muffins turning out moist and lovely.

Room Temperature Eggs: They mix better with wet ingredients, preventing curdling or lumps.
Don’t Overmix: The batter should be slightly lumpy – overworking it develops gluten and leads to a tough muffin.
Chocolate Chip Toss: Always toss chips in cinnamon before folding in so they distribute evenly and add a subtle hint of spice.
Watch Baking Time: Oven temps can vary, so start checking at 16 minutes to avoid drying out your muffins.

How to Serve Chocolate Chip Whole Wheat Muffins Recipe

chocolate chip muffins - Serving Suggestion

Garnishes

I usually skip heavy toppings because these muffins are perfect on their own, but sometimes I like a light spread of butter or a smear of almond butter to add a creamy contrast. A dusting of powdered sugar looks lovely if you’re serving for guests.

Side Dishes

Pair these muffins with your morning coffee or tea, a bowl of fresh fruit, or even alongside a smoothie for a well-rounded breakfast or snack that fills you up without weighing you down.

Creative Ways to Present

For brunch parties, I like arranging these muffins on a tiered stand with fresh berries and small bowls of nut butters and jams. Wrapping each muffin in parchment with a twine bow makes them look super cute and gift-worthy.

Make Ahead and Storage

Storing Leftovers

I keep leftover muffins in an airtight container at room temperature for up to three days. They stay moist and soft — but if I want them to last longer, the fridge works too, for about five days.

Freezing

When life gets busy, I make a double batch and freeze extras. I wrap each muffin in plastic wrap, then place them in a freezer-safe bag. They keep wonderfully for up to three months and thaw in about an hour at room temperature.

Reheating

I gently warm frozen or refrigerated muffins in the microwave for about 15-20 seconds or pop them in a toaster oven for a few minutes. It brings back that just-baked softness and chocolate gooeyness.

Frequently Asked Questions:

Can I use regular whole wheat flour instead of whole wheat pastry flour?

Yes, you can substitute regular whole wheat flour, but the muffins will be a bit denser and have a stronger wheat flavor. Whole wheat pastry flour is lighter and yields a softer texture.

What’s the best way to prevent chocolate chips from sinking?

Tossing the chocolate chips with cinnamon or a small amount of flour before folding them into the batter helps prevent sinking. This coats the chips, allowing them to suspend evenly in the batter while baking.

Can I make these muffins vegan?

Absolutely! Replace eggs with flax eggs (1 tablespoon ground flaxseed mixed with 3 tablespoons water per egg) and use vegan yogurt or homemade vegan buttermilk in place of Greek yogurt. Also, use dairy-free chocolate chips.

How long do these muffins stay fresh?

Stored in an airtight container at room temperature, these muffins stay fresh for about three days. Refrigerating extends freshness to about five days, and freezing preserves them for up to three months.

Final Thoughts

I keep coming back to this Chocolate Chip Whole Wheat Muffins Recipe because it strikes the perfect balance between wholesome and indulgent. Whether you’re serving them for breakfast, packing them for lunch, or grabbing a quick snack, these muffins never disappoint. I hope you try them out and enjoy every warm, chocolatey, slightly sweet bite as much as I do!