Bakery Style Apple Butter Muffins

Today I’ve got perfectly spiced healthy bakery style apple butter muffins. A delicious Fall muffin with that amazing crunchy domed muffin top. These muffins will be your go to breakfast this Fall!

I only first ventured into homemade apple butter last Fall and I can’t believe what I was missing out on most of my life. It’s basically fall in a jar and so delicious to bake with. I love baking with the warm spices associated with fall and winter and love eating them even more!

For another healthy recipe packed with warm spices try my cream cheese filled carrot muffins. For a more indulgent bake, try my pumpkin cake with cream cheese frosting or my chewy ginger molasses cookies.

My apple butter muffins are perfectly spiced with cinnamon and nutmeg, plus whatever spices you’ve added to your apple butter. If you don’t have homemade apple butter, store bought works as well. I know most Fall farmer’s markets tend to sell it. However, I strongly encourage you to try making your own! I make my apple butter in the instant pot and it’s so simple without much effort as I definitely do not peel my apples first. This leads to more flavour and obviously less waste as well.

These apple butter muffins are a Fall favourite in my house, especially for my daughter. She’s 1 1/2 and screams at me if I don’t share with her, even if she just had her own! These muffins will easily become a family favourite for you too as they’re delicious and make an easy, healthy snack for both adults and kids.

Bakery Style Muffins

As these are bakery style apple butter muffins, it will seem like you have too much batter. Don’t worry though, one of the tricks to a good dome on a muffin is overfilling the muffin cup. So if you want the nice dome, only make 12 muffins.

One of the other tricks to getting the perfect muffin top is to start baking the muffins at 425 F and then lower the temperature after 7 minutes. This will cause a rapid rise and help the muffin top to crisp up a little in the oven. We then drop the temperature to help them bake through without drying out or overbaking. 

While these apple butter muffins will overflow onto the tin while baking a little, I have never had a problem with them sticking and I don’t use spray or anything similar. I just use a basic muffin paper liner. Once they have cooled for 10 minutes in the pan, they should easily lift out. If they don’t, just run a butter knife or something that’s flat with a dull edge underneath and that should loosen them. I don’t recommend a sharp knife as you may scratch up your muffin tin which can also affect the non-stick coating if it has one. 

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 selenium, calcium 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.

How to Store Muffins

When storing these apple butter muffins, the first step is to ensure they are fully cooled. Storing warm muffins leads to excess moisture which will ruin the texture of your muffins and cause them to get gummy and soggy, especially on the tops. 

As muffins are generally and hopefully very moist, the easiest way to keep them from getting soggy is to store them with paper towels. 

Place a paper towel on the bottom of an airtight container or bag. I like to use an extra large reuseable bag. Then place the muffins on top in a single layer and lay an additional paper towel on top of them. Store them at room temperature for up to 3 days.

How to Freeze Muffins

The best thing about all my healthy muffins, including these bakery style apple butter muffins, is they freeze well. They’re an easy thing to whip up and meal prep for the week or month! When freezing muffins, you’ll again want to ensure they’re completely cooled. 

Once cooled, place a paper towel on the bottom of an airtight container or bag. I like to use a freezer safe extra large reusable bag. Place the muffins on top in a single layer and then place another paper towel on top. The paper towel helps to keep the excess moisture away from the muffins and helps ensure they don’t get freezer burnt. Store like this for up to 3 months.

When you’re ready to eat one or all of them, let thaw at room temperature for a couple 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.

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.

Baking Tips

  • It seems like a lot of batter but it will make 12 muffins. You need to slightly overfill each muffin cup to get the bakery style domes.
  • The turbinado sugar on top is optional but helps give the muffins a nice crunchy and slightly crispy top. Any large sugar granule, like sanding sugar, should give you the same effect.
  • Don’t overmix the batter! Fold the wet and dry ingredients together until just combined. This ensures a tender crumb rather than a tight, dense muffin.
  • 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.

Other Muffin Recipes

Pumpkin Flax Muffins
Pumpkin Oatmeal Chocolate Chip Muffins
Double Chocolate Zucchini Muffins
Chocolate Almond Banana Muffins

Today’s song is an oldie and one of my favourite all time songs. It’s also by a Canadian band! Here’s Hand Me Down World by The Guess Who. Happy baking!! **Disclaimer: Liv’s Little Muffins owns no rights to this song.

Don’t forget to leave a STAR REVIEW if you try my recipe! Follow me on Facebook or tag me on instagram @livslittlemuffins. Find more ideas on my Pinterest or Whisk.

Bakery Style Apple Butter Muffins

Olivia Daly
Perfectly spiced healthy bakery style apple butter muffins. A delicious whole grain Fall muffin with that amazing crunchy domed muffin top.
5 from 2 votes
Prep Time 5 minutes
Cook Time 19 minutes
Total Time 24 minutes
Course Breakfast, Dessert, Snack
Servings 12


  • 2 1/2 cups (300g) whole wheat flour
  • 1 1/2 tbsp (8g) ground flaxseed
  • 1 tsp ground cinnamon
  • 1/2 tsp ground nutmeg (fresh if possible)
  • 2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp salt
  • 2 large eggs
  • 1/2 cup (90g) brown sugar, packed
  • 1 cup (240g) apple butter
  • 1/3 cup (60g) canola oil
  • 1 cup (220g) unsweetened oat milk (or milk of choice)
  • 1/4 cup (55g) plain nonfat Greek yogurt
  • 1 tsp vanilla extract
  • 1 tbsp turbinado sugar (optional, to sprinkle on top)


  • Preheat your oven to 425℉. Line or spray 12 muffin tins.
  • In a medium mixing bowl, combine the flour, flaxseed, cinnamon, nutmeg, baking powder, baking soda and salt. Set aside.
  • In a large mixing bowl add the eggs, brown sugar and apple butter. Whisk until well combined. Add in the canola oil, milk, yogurt and vanilla extract. Whisk until well combined.
  • Add the dry ingredients into the wet mixture and fold until just combined. DON'T overmix.
  • Divide the batter into the 12 muffin tins. Sprinkle the turbinado sugar on top of each muffin if using and place in the oven for 7 minutes at 425℉.
  • Drop the temperature to 350℉ and bake for an additional 10-12 minutes or until a toothpick comes out clean.
  • Let cool in the pan for 10 minutes before removing to a cooling rack to fully cool. Store in an airtight container for up to 3 days or in the freezer for up to 3 months and enjoy!
Keyword Apple Butter Baking, Apple Butter Muffins, Apple Butter Recipes, Bakery Style Apple Butter Muffins, Healthy Apple Butter Muffins, Whole Grain Apple Butter Muffins
Tried this recipe?Let us know how it was!

Nutrition Facts

Serving Size1muffin
Amount Per Serving
% Daily Value *
Total Carbohydrate34g
Dietary Fiber3.6g
Total Fat7g
Saturated Fat0.8g
Trans Fat0.02g

1 Comment

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating