It’s time for another muffin recipe and these are my son’s favourite. They’re my version of bakery style chocolate chip muffins but we’ve swapped out some things like butter and all purpose flour to make these a healthier option.
These bakery style chocolate chip muffins are the perfect breakfast, snack on the go, or school lunch snack. Making healthier muffin recipes is actually what motivated me to start this blog and I feel like a chocolate chip muffin is just a staple. Although these are a healthier option, I promise they won’t leave you wanting something more. These muffins are delicious, with big crunchy tops just like at a bakery.
My whole grain bakery style chocolate chip muffins are super simple to make, kid approved and freezer friendly. They’re also a great snack to keep in the freezer if you’re about to become a parent. A healthier late night snack is always a necessity!

For a different day, check out my bakery style apple butter muffins or my bakery style oatmeal muffins, both of which are a healthier muffin option! If you’d like a more indulgent muffin, try my Tim Horton’s copycat chocolate chip muffins. These are just like any bakery muffin you know and love.
How to Get the Tall Muffin Tops
There’s a couple important steps here besides the recipe itself that will assure you tall bakery style tops. First is letting the batter rest for 15-20 minutes.
Next is starting the oven temperature higher at 425°F, forcing the muffins to rise quickly. Just make sure to turn the temperature back down after 7 minutes or they’ll become dry.
Third, is filling each one so it’s almost overflowing. This is also why you need to let the batter rest. The water molecules will start to absorb leading to a thicker batter. Then you can overfill without making a big mess.
Last is optional and it’s only filling 6 of the muffin cups in your pan. So you fill every other cup. This allows heat to better spread and gives the muffins more room to grow. You can skip this step but your muffins won’t rise as much and may bake into each other a little.
Also, if you really want the look of bakery chocolate chip muffins, then add the sanding or turbinado sugar as well as additional mini chocolate chips on top.
How to Properly Measure Flour
So when it comes to measuring flour, the most accurate and easiest way is to use a kitchen scale. I always use a scale and could never go back to measuring in cups. It’s such a hassle and way more dishes!
If you don’t own a scale, there are a couple steps to properly measure flour as it becomes compacted just sitting in the bag or container. I highly recommend you follow these as just scooping flour out of the bag can potentially lead to at least an additional 1/4 cup of flour. This equals dry and dense baked goods which is not what anybody is going for.
1. Fluff the flour by giving it a mix with a whisk or fork.
2. Spoon the flour into your measuring cup.
3. Level the excess flour off using a butter knife. (With the back of the knife level to the top of the measuring cup, run it over top, pushing the excess flour back into it’s container.)
4. Repeat until you’ve measured the amount the recipe calls for.

How to Store Muffins
When storing these bakery style chocolate chip muffins, follow these steps:
- Fully cool the muffins, otherwise they’ll get gummy and soggy.
- Place a paper towel on the bottom of an airtight container or bag.
- Put the muffins on top of the paper towel.
- Lay another paper towel on top of the muffins.
- Seal and keep at room temperature for up to 3 days.
How to Freeze Muffins
If you want to freeze these, follow these steps:
- Fully cool the muffins
- Place a paper towel on the bottom of an airtight container or bag.
- Put the muffins on top of the paper towel in a single layer.
- Lay another paper towel on top of the muffins.
- Seal and keep at room temperature for up to 3 days.
- To eat, take amount you need out and let thaw at room temperature for 2 hours or heat in the microwave in 20 second increments. Be cautious if using the microwave when feeding children or toddlers, it can leave hot spots.

Benefits of Whole Wheat vs White Flour
When baking healthier snacks, treats or breakfasts, I’m a big fan of using whole wheat flour instead of all purpose flour, also known as white flour. There are many benefits to this including a higher concentration of minerals like copper, magnesium and iron. This is important for me personally as like many women, I’ve had issues with low iron in my life.
There is also a larger source of B vitamins in whole wheat flour which provides energy. Whole wheat flour has a higher protein content as well as more fibre, both of which can keep you feeling full longer. Another great thing about whole wheat flour is it can add a little extra flavour bringing a hint of nuttiness to certain bakes.
The only cons of using whole wheat flour that I know of is sometimes it can make a recipe more dense, which is why I typically add more moisture to my recipes. In doing this, I generally don’t notice that I’m eating a whole wheat flour muffin instead of a white flour muffin.
The other downside is I know everybody doesn’t keep whole wheat flour on hand. Well, I never used to either and now I can’t imagine not having it in the house. I buy a large 10kg bag for the exact same price as an all purpose bag of flour and have never had it go bad on me. I highly recommend keeping some on hand so you can make guilt free muffins, quick breads or whatever you want! In saying this, if the recipe doesn’t call for it, I don’t recommend swapping whole wheat flour for white flour, they’re generally not a 1 to 1 substitute.
If you’d like more information on the nutritional benefits, head to https://www.hsph.harvard.edu/nutritionsource/what-should-you-eat/whole-grains/. There are lots of great sources of nutritional information on the Harvard website that is backed up by multiple sources.

Baking Tips
- Make sure not to overmix the batter or you will end up with a very tough, dense muffin. Gently fold the batter until just combined.
- For a taller dome and to avoid them baking into each other a little, bake them in every other tin, so only 6 muffins per pan.
- Ensure all your ingredients are at room temperature for the best bake and texture.
- Mini or regular chocolate chips work but I prefer mini as they disperse better without having to use as many.
- I create my recipes based off weights so I recommend measuring by weights if you own a scale. It’s actually so much easier and makes for much less cleanup. I wish I had baked by weight from the beginning, I could never go back now.

More Healthier Recipes
Today’s song is by one of my all time favourite bands. They are so fun to see live in a pub so if you ever get the chance, go! Here’s Workin’ Man Zombie by the 4onthefloor. Happy baking!! **Disclaimer: Liv’s Little Muffins owns no rights to this song.
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Healthier Bakery Style Chocolate Chip Muffins
Ingredients
- 2 cups (240g) whole wheat flour
- 1/4 cup (35g) cornstarch
- 2 tsp baking powder
- 1/2 tsp baking soda
- 1/4 tsp salt
- 2 large eggs
- 2/3 cup (120g) light brown sugar, packed
- 1/3 cup (60g) canola oil (or neutral oil like avocado)
- 1 cup (220g) plain Greek yogurt (I typically use nonfat)
- 3/4 cup (165g) unsweetened oat milk (or any kind of milk)
- 2 tsp vanilla extract
- 1/2 cup (80g) chocolate chips (I like mini chocolate chips)
- Sanding sugar for topping (optional)
Instructions
- In a medium mixing bowl, add the flour, cornstarch, baking powder, baking soda and salt. Whisk to combine and set aside.
- In a large mixing bowl, add the eggs and sugar. Whisk until well combined. Add the oil, yogurt, milk and vanilla extract and whisk until combined.
- Add the dry ingredients into the wet mixture and fold until just combined. Add the chocolate chips and fold to combine, just don't overmix! Let batter rest for 15 minutes and preheat the oven to 425℉ while you wait.
- Line or spray 12 tins on 2 different pans, alternating so there's space between each muffin or 12 tins in one pan (*see notes). Fill each tin so it's almost at the top. Use all of the batter! As we've rested the batter, it won't actually spill out the sides. Then top each muffin with sanding sugar if you like.
- Bake at 425℉ for 7 minutes and then without opening the oven door, drop the temperature to 350℉ and bake for an additional 9-11 minutes or until they spring back when touched or a toothpick comes out clean. Allow to fully cool before storing in airtight container for up to 3 days and enjoy!
These muffins are one of my son’s favourites and I love packing then as a healthier “treat” in his lunch.
If you give these a try, let me know what you thought with a rating and start review!