Cream Cheese Filled Carrot Muffins

Whenever I’m craving carrot cake, one of my all time favourites’, these carrot muffins are a great healthier option!! One of the reasons I love carrot cake so much, besides the warm spices, is how well it pairs with cream cheese frosting. So obviously, I had to incorporate a delicious, sweet cream cheese filling into these muffins.

For a different dessert for breakfast option, try my coconut cream pie overnight oats or my black forest overnight oats. Or for a different veggie filled muffin, try my double chocolate zucchini muffins or my pumpkin flax muffins.

These carrot muffins make a great snack or breakfast option as they’re actually quite filling thanks to being chocked full of carrots and oats. As I was developing this recipe, I kept adding more carrots each trial run. I wanted to get the nutritional value from the carrots but I also like when you can taste the carrots in a carrot muffin or cake. Whoever thought of pairing carrots with all those warm spices like ginger and cinnamon was a genius in my books, nom nom nom!!

I’m happy to report these carrot muffins with the cream cheese centre are kid approved as well. Both my toddler and 5 year old enjoy them! My son, who’s 5 actually loves cream cheese frosting so I just told him the frosting was on the inside instead of on top. He was so excited and devoured the whole muffin!

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 There are lots of great sources of nutritional information on the Harvard website that is backed up by multiple sources.

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.

Front view of an unwrapped cream cheese filled carrot muffin. More muffins in the background.

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

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

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

The best thing about all my healthy muffins, including these carrot 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.

  • 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.
  • You can use either low fat or regular cream cheese for the filling. I have low fat in the recipe just to make them a little healthier but either option will be delicious!
  • To get the cream cheese to sit in the centre, I only fill the muffin cups about 1/3 of the way. Make sure the whole bottom of the cup is covered. Then, I use a tsp to scoop half balls right into the centre. When you put the rest of the batter in, make sure you completely cover the cream cheese. This also helps keep it creamy versus it baking and getting kind of dry.
  • 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.

Funfetti Blondies
Creamy Lime Bars

My song today is a slower but beautiful song. This is one of my favourite songs to sing along with, it’s just so pretty and soothing. Hope you enjoy Down in the Valley by The Head and the Heart! 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.

Cream Cheese Filled Carrot Muffins

Olivia Daly
These carrot muffins are packed full of carrots and a delicious cream cheese filling. A healthier option to a piece of carrot cake!
5 from 2 votes
Prep Time 15 minutes
Cook Time 33 minutes
Total Time 48 minutes
Course Breakfast, Dessert, Snack
Servings 12 muffins


Cream Cheese Filling

  • 115g/4oz low fat cream cheese, room temp
  • 1 1/2 tbsp (32g) honey
  • 1/2 tsp vanilla extract


  • 2 large eggs
  • 1/4 cup (45g) canola oil
  • 1/3 cup + 1 tbsp (136g) honey (maple syrup if feeding to child under 1)
  • 1 cup (215g) unsweetened almond milk (or milk of choice)
  • 1 tsp vanilla extract
  • 1 1/3 cup (160g) whole wheat flour
  • 3/4 cup (90g) quick oats
  • 2 tsp ground cinnamon
  • 1 tsp ground ginger
  • 1/4 tsp ground cloves
  • 1/4 tsp ground nutmeg
  • 2 1/4 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp salt
  • 2 1/2 cups (300g) grated carrot, packed (about 3-5 carrots)


  • Line or spray 12 muffin tins. Preheat your oven to 350℉.
  • In a small mixing bowl, add your cream cheese, 1 1/2 tbsp honey and 1/2 tsp vanilla extract.
  • Using a hand mixer, mix at medium speed until creamy. Set aside.
  • In a medium mixing bowl, combine your flour, oats, cinnamon, ginger, cloves, nutmeg, baking powder, baking soda and salt. Set aside.
  • In a large mixing bowl, combine the eggs, canola oil, honey, almond milk and vanilla extract. Whisk until well combined.
  • Add in the grated carrot and whisk until well combined.
  • Add the dry ingredients to the wet ingredients and fold until combined.
  • Fill each tin about 1/3 full, ensuring the bottom is completely covered.
  • Then, using a tsp or tsp sized scoop, scoop a heaping tsp of cream cheese mixture onto the top of the batter of each muffin tin. Try and keep it in a ball shape as this helps it stay in the middle of the muffin.
  • Put the remaining batter into each tin, ensuring the cream cheese is completely covered.
  • Cook the muffins for about 32-34 minutes or until the sides are set. It is a little trickier to tell if the centres are fully baked as the cream cheese will still have a little jiggle in the centre, but this is what we want.
  • Cool the muffins in the tins for 5 minutes, then move to a cooling rack to completely cool. Store in an airtight container for 1 day or in the freezer for up to 3 months.
Keyword Cream cheese filled carrot muffin, Whole wheat flour carrot muffins
Tried this recipe?Let us know how it was!

Nutrition Facts

Serving Size1muffin
Amount Per Serving
% Daily Value *
Total Carbohydrate30.23g
Dietary Fiber3.43g
Total Fat7.04g
Saturated Fat1.58g
Trans Fat0.02g


  1. 5 stars
    It’s really good, but I put too much texture at first so the cream cheese was on top of the muffins.

  2. Hi! I am going to try this recipe but was wondering if you have tried coconut oil instead of the canola oil? And would the measurement be the same? Thanks!

    • Hey there! I haven’t but I think it should be a 1:1 ratio. As coconut oil is more solid at room temperature it may alter the texture a little so perhaps try warming it so it’s liquid first? This should make it easier to fully incorporate. Hope this helps and let me know how they turn out!

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