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Healthy Zucchini Applesauce Muffins Recipe

Zucchini applesauce muffins are a healthy choice to enjoy for breakfast or a snack, but still sweet and delicious for kids and adults alike. Moist breakfast bites with veggies made in a mini or regular muffin pan. Just another version of our moist zucchini bread recipe we came up with this week, but smaller.

apple zucchini muffins

Looking to make a healthier muffins with whole wheat flour but still want it to taste delicious? It must right? These zucchini applesauce muffins will turn you into a believer that breakfast and vegetables go together. Just one of the best muffin recipes on our site. (affiliate links present)

Applesauce Muffins

I mean you could really swap out this veggie for carrots instead if you wanted to, or use half and half! There’s nothing better than “hiding” a bit in a recipe that your kids say YUM to right?? It not only adds nutrition, but a bit of texture too and added moisture so it is tender for every bite.

This size my kids love because they can grab one and go in the mornings on the way to school or practice. You can make them large, regular size like seen here or they love mini muffins as well. We often times start with this easy muffin recipe you can add all sorts of fruits and veggies into them.

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Now let’s talk a bit about my favorite things when it comes to muffins though shall we?

  1. You really should get a 24 cup muffin pan, or opt for a quicker baking time with mini muffins.
  2. I ALWAYS use muffin liners and you should too. They make cleanup easier and grab and go breakfasts a thang. 😉
    1. No pan, no problem! You can use stiffer or silicone self standing muffin cups instead!
muffin recipe

Zucchini Muffins with Applesauce

Often times two are used like in our zucchini carrot muffins. It’s a great way to “hide” goodness from the kiddos.

To make it on the healthier spectrum, the binder was swapped out this time for whole wheat flour instead. I have this flour substitute chart if you’d rather use a different type. This is the only one I have used though so I cannot vouch for how another one might do with the other ingredients listed.

If you haven’t used this darker alternative it does add a lot of healthy aspects to your sweet baked goods. The texture is a bit heavier so you’ll notice that it’s a bit more dense when done. Offering a deeper flavor than it’s white counterpart, it may become a new favorite tweak you can enjoy beyond this one.

zucchini muffin recipe

Zucchini Applesauce Bread

Yes you could very well bake this in a loaf pan but it would take much longer. Typically when I make something larger like our zucchini pineapple bread it will take closer to 50 minutes until a toothpick will come out clean.

I personally prefer bite sizes like this so we can grab and go in the morning, and freeze them easier as well.

  1. Whole wheat flour should still be measured properly so you don’t add too much and make it dense.
    • healthier substitute to all purpose flour that is what without nutrients
  2. Wheat germ will add nutrients, folate, magnesium, phosphorus and zinc into the mix.
  3. Shredded zucchini is easiest to do on a wad of folded paper towels. Then fold it over and gently press down to soak up the excess water, you don’t want that added into your batter.
  4. Milk
  5. White sugar
  6. Applesauce can be jarred or make Instant Pot applesauce the day before. Use some with this and save the rest for a healthy snack.
  7. Egg
  8. Baking powder and a bit of salt
  9. Large bowl

Always add veggies at the end and gently fold in so they don’t get too broken down. It is really important to take the extra minute or two to reduce the liquid too. With just a few paper towels you can gently press down and it will absorb that excess water on the outsides of your grated pieces.

Zucchini Applesauce Muffins

How do you make applesauce muffins from scratch?

We will show you how to do just that right here. Yes you could leave out the shredded vegetables all together, or swap those out for shredded carrots too! It’s just a nice way to add texture and moisture. There isn’t a huge difference in taste either way believe it or not, mostly just the color.

Can you substitute applesauce for sour cream?

You can! It is a great way to reduce the fat content but still add moisture and a creamier nature to your baked goods. Of course the latter will give it a different look and flavor vs. it’s fruit counterpart.

You could add 1/4 cup of chocolate chips too if you wanted. I like mini semi sweet if I am doing that. I am not a crushed nuts in my baked goods gal but that would be fine too. If making a double batch follow the same instructions. You could package half of them in freezer bags to save for later too.

To defrost take the bag out and let them come to room temperature. Then enjoy or you could warm each in the microwave too in 20 seconds or so. A great thing to do if you have a vegetable garden and don’t want food wasted. Batch cook a few dozen and freeze them for later in the year.

Healthy Zucchini Muffins

Healthy Applesauce Muffins

Let’s talk about baking the perfect muffin. I will say that I am very particular when it comes to this snack. I grew up eating them a lot as a child and the worst was patiently waiting for them to bake after spending the afternoon making the batter and they cooked too long. The worst!! The last few minutes are critical and you need to pay attention.

Baking is now something I do a lot with my girls and I have taught them these same kitchen hacks. We do this A LOT so I do have a few tips you should follow.

  • Use muffin liners in your muffin pan, I prefer this over spraying the inside with non stick cooking spray.
  • Do NOT over-bake them. Best way to do this is to set the cook time for the minimum amount listed in your recipe. Remember that ovens vary just a bit, and altitude will change how long is necessary too.
  • Check for doneness with your finger! That is right, it works better than a toothpick inserted. If you gently touch the middle of one and it springs back, take them out immediately! If it stays down, give it another 1-2 minutes and touch gently again.
  • Remove immediately from the pan! Once they spring back, take the muffin tin our and flip it over. Flip them back on to their bottoms and on a cooling rack to cool completely.

Follow these tips so they turn out great every time you make them, no matter what type you make. Using your finger to test the tenderness is probably #1 on the importance scale of things. It is better than using a knife or toothpick because it can dry them out quicker than really feeling where they are at.

applesauce zucchini muffins

Applesauce Muffins Baby

If you want to know how long to bake mini muffins we have the answer here. Great for little ones or for on the go snacks. Here are quick step by step instructions but exact amounts and steps are listed below in the printable recipe card for you.

  1. Preheat oven to 400 degrees F. In a bowl combine a whisked egg, then add sugar, milk and applesauce.
  2. Mix in wheat germ and salt. In a bowl mix together wheat flour and baking powder, then gradually add this into the mix and fold together until incorporated.
  3. Shred zucchini on paper towels. Then roll them up and gently press down to absorb the water before adding into your batter.
  4. Gently fold together, if adding crushed nuts add now too.
  5. Use muffin liners and fill 3/4 of the way full. Bake for 17-21 minutes or until muffin comes out clean with toothpick inserted or when touched in the center the muffin springs back.
  6. Remove from muffin pan and cool, enjoy.

After this try another one of our favorites like these pumpkin zucchini muffins! A normally favorite Fall flavor you can buy cans of puree year round now which I love. I could eat these every week because they are just that good. The duo of shredded zucchini with the second veggie flavor is something that may sound odd but will surprise you non the less.

Pumpkin Zucchini Muffins

Zucchini Apple Muffins

Need something quicker for guests that arrived unexpectedly?? Throw together these 2 ingredient pumpkin muffins for them. OH MY do they taste homemade but kinda’ aren’t. Nobody will know the difference though, love that. I haven’t added veggies to those but could follow the same suggestions here and go for it.

Always remember to press inside a few paper towels or cheesecloth to dry them out before folding in at the very end. About 1/2 cup would do it in this case.

Have brown nanners? Don’t throw those babies out, instead make a batch of our zucchini banana muffins for breakfast. You can kinda’ transform any of these into more of a dessert with a dollop of cream cheese frosting so yay!

applesauce zucchini muffins

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apple zucchini muffins
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5 from 4 votes

Zucchini Applesauce Muffins

Zucchini applesauce muffins are a healthy choice but still sweet and delicious for kids and adults alike. Moist breakfast bites with veggies.
Course Breakfast, Dessert
Cuisine American
Keyword applesauce, bread, healthy, muffins, zucchini
Prep Time 15 minutes
Cook Time 18 minutes
Servings 12
Calories 124kcal
Author The Typical Mom




  • Preheat oven to 400 degrees F. Beat egg in a bowl, then add sugar, milk and applesauce.
  • Mix in wheat germ and salt. In a bowl mix together baking powder and wheat flour, then gradually add this into the mix and fold together until incorporated.
  • Shred zucchini on paper towels. Then roll them up and gently press down to absorb the water before adding into your batter.
  • Gently fold together, if adding crushed nuts add now too.
  • Use muffin liners and fill 3/4 of the way full. Bake for 17-21 minutes or until when touched in the center gently the muffin springs back. (check at 17 minutes, oven temps vary and you don't want to dry them out)
  • Remove from muffin pan and cool, enjoy.


Nutrition Facts
Zucchini Applesauce Muffins
Amount Per Serving (2 oz)
Calories 124 Calories from Fat 18
% Daily Value*
Fat 2g3%
Saturated Fat 1g6%
Trans Fat 1g
Polyunsaturated Fat 1g
Monounsaturated Fat 1g
Cholesterol 16mg5%
Sodium 114mg5%
Potassium 308mg9%
Carbohydrates 24g8%
Fiber 2g8%
Sugar 10g11%
Protein 4g8%
Vitamin A 87IU2%
Vitamin C 3mg4%
Calcium 93mg9%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.
easy zucchini muffins
Recipe Rating

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Sunday 18th of February 2024

These muffins are so moist and flavorful, with a perfect balance of sweetness. The combination of zucchini and applesauce makes for a guilt-free treat that I can't get enough of!


Sunday 18th of February 2024

Awesome muffin recipe! Not only did they taste good and are super healthy, but our kids loved them too! Thank you so much!


Sunday 18th of February 2024

As soon as I saw this, I knew I had to try it. These are spectacular - thanks for a wonderful recipe!


Sunday 18th of February 2024

These muffins were something that my toddler loved! Thank you so much for sharing this recipe :)

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