Lunchbox Muffins Recipe

These lunch muffins are a fun way to keep lunch interesting for the kids!

I remember when I was a kid, the best part of bringing lunch from home was when I would find a sweet treat in my lunch box. But even back then, my mom and grandmother were all about making sure I got a good, home-cooked meal. Even in said lunch box. This was not always a happy thing for me. But the rare and occasional sweets were always something I hoped for. Something I looked forward to.

A close up shot of these Clean Eating Lunchbox Muffins lined up on a cutting board. Each muffin has a red and white checkered paper liner.

Now that I have my own munchkin, I see the same hopeful look in his eyes when he checks to see what I’m packing in his lunch for the day.

And while I’m usually a pretty strict mom, I hate seeing that look of disappointment on his face when he doesn’t get something he likes. So I decided to create something that I would feel better about giving him. Something that is mildly sweet without giving him such a large sugar rush that he can’t sit still in class. So I kept the sugar relatively low as well as the portions small by making these mini muffins.

Several Clean Eating Lunchbox Muffins surround a reusable juice box filled with milk. A few of the muffins sit in a lunchbox sized container to show their size. There is a white flower off to the side.

They are perfectly sized for a lunch box! They don’t take up much room, they are totally kid-sized and give my lil’ guy just enough sweet to put a smile on his face. Yay, mom!!

More Healthy Muffin Recipe

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Clean Eating Lunchbox Muffins Recipe

Lunchbox Muffins Recipe

A lunch box friendly, low sugar, small portioned treat you won’t feel bad about giving your kids.
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Course: Dessert, Snack
Cuisine: American
Prep Time: 10 minutes
Cook Time: 30 minutes
Total Time: 40 minutes
Servings: 36 mini muffins
Calories: 60kcal


  • 1 Mini muffin pan


  • 1 large egg
  • ½ cup honey
  • ¼ cup oil
  • ¾ cup milk
  • ½ cup unsweetened apple sauce
  • 2 cups whole wheat pastry flour (affiliate link)
  • 2 tsp. baking powder
  • 1 tsp. ground cinnamon
  • 1 cup cherries (pitted and chopped – or any fruit you prefer)


  • Place all ingredients except the cherries in a blender and blend until smooth.
  • Pulse in the cherries and spoon the batter into a lined mini muffin pan.
  • Bake at 350 F. for 25-30 minutes or until cooked through.
  • Cool completely before removing liners from muffins.


Please note that the nutrition data below is a ballpark figure. Exact data is not possible.


Serving: 1muffin | Calories: 60kcal | Carbohydrates: 10g | Protein: 1g | Fat: 2g | Cholesterol: 5mg | Sodium: 4mg | Potassium: 73mg | Sugar: 4g | Vitamin A: 20IU | Vitamin C: 0.3mg | Calcium: 23mg | Iron: 0.3mg

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  1. I was curious what other fruits you would recommend if we wanted to substitute something else for the cherries?

    1. The Gracious Pantry says:

      Melody – Blueberries would be wonderful. Raspberries, apples, even chunks of banana if you cut them up small. Although you may have to cook them a little longer with the banana.

  2. Nancy Payne says:

    These are delicious! I used apples instead of cherries. My kids love them!
    It was kind of messy using my ninja blender. I’m wondering if they would turn out as well if I just mixed by hand?

    1. The Gracious Pantry says:

      Nancy – I’m sure they’d be fine. I did it in a ninja too and didn’t have a problem, but your blender may be different. I would just be sure to mix really well to get the batter very smooth. Other than that, there’s no reason you couldn’t do this by hand. Glad you enjoyed them! 🙂

  3. I have only a regular size muffin pan. Do you think they would come out just as good? How long should I bake them?

    1. The Gracious Pantry says:

      Rosanna – I’m sure they would be fine. I would bake them for the same time and then check them. If they aren’t done, Keep baking and check about every 5 minutes until done.

  4. Is there something I can use instead of apple sauce?

    1. The Gracious Pantry says:

      Jules – Applesauce is typically the replacement for oil or butter. In this recipe, you could replace it with 1/2 the amount of either. If you can do dairy, I recommend the butter.

      1. should the butter be melted or softened?

        1. The Gracious Pantry says:

          Jules – Melted is probably a good choice. Let me know how they turn out!

  5. jeannette says:

    These sound yummy!! For Gluten Free version, do you think they would work with coconut or almond flour?

    1. The Gracious Pantry says:

      Jeannette – I would probably have to recommend a combo of both since coconut flour is EXTREMELY absorbent and almond flour absorbs almost nothing. However, I haven’t tried it so I’m not sure how it would work out. If you do want to try it, I would recommend starting with 1 3/4 cups almond flour and 1/4 cup coconut flour and see how it does.

  6. Can I use regular white flour for these?

    1. The Gracious Pantry says:

      Abby – I suppose you could, but it wouldn’t be clean if you do.