Zucchini applesauce muffins are a healthy choice but still sweet and delicious for kids and adults alike. Moist breakfast bites with veggies.

Looking to make a healthier muffin 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??
Just another version of our moist zucchini bread recipe we came up with this week, but smaller. This size my kids love because they can grab one and go in the mornings on the way to school or practice.
Let’s talk a bit about my favorite things when it comes to muffins though shall we?
- You really should get a 24 cup muffin pan, or opt for a quicker baking time with mini muffins.
- I ALWAYS use muffin liners and you should too. They make cleanup easier and grab and go breakfasts a thang. 😉
- No pan, no problem! Use these self standing muffin cups instead!
- This is the best way to store leftovers so they don’t get smushed!

Zucchini Muffins with Applesauce
We often times start with this easy muffin recipe you can add all sorts of fruits and veggies into them. 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.

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.
- Whole wheat flour should still be measured properly so you don’t add too much and make it dense.
- Wheat germ will add nutrients, folate, magnesium, phosphorus and zinc into the mix.
- 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.
- Milk
- White sugar
- Applesauce can be jarred or make Instant Pot applesauce the day before. Use some with this and save the rest for a healthy snack.
- Egg
- Baking powder and a bit of salt
- Large bowl
Always add veggies at the end and gently fold in so they don’t get too broken down.

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.
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. 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.

Healthy Applesauce Muffins
Let’s talk about baking the perfect muffin. 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.

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.
Time needed: 18 minutes.
Zucchini Applesauce Muffins
- Prepare
Preheat oven to 400 degrees F. In a bowl combine a whisked egg, then add sugar, milk and applesauce.
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.
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. - Bake
Use muffin liners and fill 3/4 of the way full. Bake for 18-21 minutes or until muffin comes out clean with toothpick inserted or when touched in the center the muffin springs back.
Remove from muffin pan and cool, enjoy.
After this try another one of our favorites like these 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.
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!
Want to see a few of my favorite things that I am totally obsessed with?? Take a peek and see how many you might already have…twinsies!
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Zucchini Applesauce Muffins
Ingredients
- 1.5 c whole wheat flour
- 1/2 c wheat germ
- 1.5 c zucchini shredded and pressed in paper towels
- 1 c milk
- 1/2 c sugar
- 1/4 c applesauce
- 1 egg
- 4 tsp baking powder
- 1/2 tsp salt
Instructions
- 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 18-21 minutes or until when touched in the center gently the muffin springs back.
- Remove from muffin pan and cool, enjoy.