Healthy Fruit on the Bottom Yogurt


Published: November 28, 2024 · Updated: November 28, 2024 by Mark & Sacha — This post may contain affiliate links. Read our full disclosure.

If you enjoy fruit bottom yogurt cups from the store, you'll love this healthy fruit on the bottom yogurt recipe that you can make at home! These DIY yogurt cups are made with real fruit, minimally sweetened and thickened with chia seeds rather than cornstarch. They are a great nutritious snack or breakfast for children and adults!

6 cups of yogurt with fruit compote on the bottom, in 3 different flavors.

Love store-bought fruit on the bottom yogurt, but not the price tag or added sugar? If so, this homemade version is the perfect solution. Not only is it easy to make, but it only requires four simple ingredients, and can easily be customized to suit your preferences.

These yogurt cups have become a staple in our house, and they are a great addition to my children's breakfast or after-school snack. We love trying new fruit combinations!

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Why You'll Love This Recipe

  • Simple ingredients: Unlike store-bought versions, which can contain lots of unnecessary ingredients, this recipe only contains four—including real fruit and chia seeds, which provide a boost of fiber.
  • Low added sugar: Store-bought fruit bottom yogurt is often high in added sugars, but this homemade version is not overly sweet, and its sweetness comes from real fruit a small amount of honey that can be adjusted (or omitted) according to your preference.
  • Nutritious breakfast or snack: My kids love having these yogurt cups for breakfast or as an after-school snack. They even pack them in their lunchboxes on occasion.
  • Easy to make and customize: These yogurt cups are super simple to make, and would be a great way to get your kids helping out in the kitchen. They are also a lot more versatile than store-bought versions when it comes to fruit combinations.

Love yogurt? Check out this simple recipe for Homemade Drinkable Yogurt!

Required Ingredients

Ingredients to make fruit on the bottom yogurt.
  • Fruit: I like to use frozen fruit because it is cost-effective and available year-round, but fresh fruit would work as well. Berries work especially well for this recipe because they are flavorful and break down easily, but you can also use stone fruit like cherries, apricot or peach. The only fruit I wouldn't recommend are banana and citrus (though you could always add some citrus zest if you like the flavor).
  • Honey: I generally use honey for this, but maple syrup or agave syrup could work too. If you are making this for a child under 12 months old, skip the honey and use one of the alternatives, as honey can cause botulism in babies under one year of age.
  • Chia seeds: White or black chia seeds are both fine—they are identical except for the color. I typically use black chia seeds, but if you are using a light-colored fruit like peaches and you find it visually off-putting to see black seeds in your fruit compote, try using white chia seeds instead.
  • Yogurt: I like to use plain homemade Greek yogurt for this recipe, though store-bought would work just as well. I prefer Greek yogurt because of its thicker consistency and higher protein content, but you can also use regular yogurt. Full-fat and low-fat are both fine, as is using vanilla yogurt instead of plain (but you'll need to reduce the amount of honey to compensate for the added sweetness).

The full ingredient list, quantities and instructions can be found in the recipe card.

Variations & Substitutions

  • Make it lactose-free: Use lactose-free yogurt or Greek yogurt. (If you like to make your own yogurt, you can make it lactose-free by using lactose-free milk and starter.)
  • Make it dairy-free: Replace the yogurt with plant-based yogurt, such as coconut milk yogurt.
  • Make it vegan: Swap the honey for agave or maple syrup, and use store-bought or homemade vegan yogurt.
  • Increase the protein content: Stick with Greek yogurt instead of regular yogurt. If you wish, you can also sweeten the yogurt with protein powder instead of honey.
  • Switch up the flavor: My favorites are raspberry and cherry, but feel free to use any type of fruit you have on hand, or even a combination of multiple types of fruit. You can also add citrus zest or flavored extracts.

How to Make Fruit on the Bottom Yogurt (Step-by-Step)

Cherries being cooked in a small saucepan.

Step 1: Cook fruit. Place the fruit in a small saucepan and cook it on medium heat for 5-10 minutes, stirring regularly, until it has softened and released its juices. If the fruit isn't very "juicy" and you find that it is sticking to the bottom of the saucepan, add a couple tablespoons of water to help break it down.

Cooked cherries broken down with an immersion blender.

Step 2: Blend or crush fruit (optional). If needed, use a potato masher or immersion blender to break up any large chunks of fruit that haven't broken down during the cooking process. (This step is rarely necessary for berries.) You can also blend the mixture in a blender or food processor for a few seconds before returning it to the saucepan.

Prepping Your Fruit

Frozen fruit can generally be used right out of the bag, but if you are using fresh fruit that isn't berries, make sure to remove any stems, pits or seeds and chop it into smaller pieces before using. If needed, you can also remove the skin of the fruit.

Cherry compote with chia seeds and honey.

Step 3: Add honey and chia seeds. Add ½ tablespoon of honey, tasting the fruit mixture and adding more honey if needed to remove excess tartness. (Tarter fruit like raspberries will require more sweetener.) Stir in the chia seeds and cook for 3-5 more minutes on your element's lowest heat setting, stirring frequently. Remove from heat and place in the fridge to cool.

Bowl of yogurt with honey mixed in.

Step 4: Sweeten yogurt. While the fruit compote is cooling, pour the yogurt into a bowl and stir in the remaining 1 ½ tablespoons of honey. Taste and adjust the sweetness as needed, bearing in mind that the yogurt will be combined with the fruit compote when eaten, so it should only have a light sweetness on its own.

Cherry compote divided into 6 small containers.

Step 5: Divide compote into containers. Once the compote has cooled, divide it equally between six sealable 4-ounce mason jars or containers—you will have about 1 ½ to 2 tablespoons per jar.

Assembled fruit on the bottom yogurt cups.

Step 6: Add yogurt. Add about ⅓ cup of the sweetened yogurt on top of the fruit compote in each jar, dividing it equally between all six. Place the yogurt cups in the fridge until ready to consume.

My kids are huge fans of these yogurt cups, and they love trying new fruit combinations! I generally make a couple different flavors at a time when I am prepping food for my family.

Open raspberry fruit bottom yogurt cup, with fruit and yogurt mixed.

Helpful Tips

  • Thaw larger frozen fruit (optional): While this isn't strictly necessary, especially when using smaller fruit like berries, it can help large pieces of fruit break down and release their juices more easily. I usually do this for frozen peach slices since they are larger and "drier" than berries.
  • Don't overcook the fruit: The fruit should be cooked just until it releases its juices, but not long enough for those juices to evaporate, or the compote will be too thick and won't mix with the yogurt properly. If it seems too dry, add a bit of water to the fruit (while it's cooking) or to the finished compote (before you divide it between the containers).
  • Don't add too much sweetener: When you are stirring honey into the yogurt, make sure not to add too much. The yogurt should only taste slightly sweet, as it will be combined with the fruit compote, and you don't want the sweetness to be overbearing once they have been stirred together.
  • Make the perfect compote: Your compote should be jam-like and soft enough to mix into the yogurt, but still contain small chunks of fruit. If you are using an immersion blender to break down the fruit, don't over-blend—the fruit should still be slightly chunky, not smooth and purée-like (unless you want it to be). If the compote is too thick after cooling, stir in small amounts of water until it reaches the desired consistency.

Looking for more healthy breakfast recipes? Check out this Berry Baked Oatmeal or these Pomegranate-Blueberry Overnight Oats!

Storage & Serving Instructions

This recipe yields six individual portions that can be kept in 4-ounce mason jars or plastic containers. (I prefer glass as a general rule, but I typically use plastic for this recipe in case my kids want to bring the yogurt cups to school.)

To save your yogurt cups for later, seal the jars or containers with lids and place them in the fridge for up to a week. When serving, stir the fruit and yogurt together to distribute the flavor throughout.

You can also add some granola, nuts or seeds to turn your yogurt cups into fruit parfait.

Frequently Asked Questions

Homemade fruit bottom yogurt cups will last up to a week when stored in sealed jars in the refrigerator.

Though you are welcome to eat the yogurt and fruit separately if you wish, fruit bottom yogurt cups will taste better if you use a spoon to stir the two layers together and combine the flavors.

Have a question that wasn't answered here? Let us know in the comments and we'll be happy to help!

If you have tried this Fruit on the Bottom Yogurt or any other recipe on our website, please let us know how it went in the comments below. We can't wait to hear from you!

6 cups of yogurt with fruit compote on the bottom, in 3 different flavors.

DIY Fruit on the Bottom Yogurt

Sacha
These healthy fruit on the bottom yogurt cups are made with real fruit, minimally sweetened and thickened with chia seeds rather than cornstarch for an added boost of fiber! They are perfect for breakfast or as an after-school snack.
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Prep Time 5 minutes
Cook Time 10 minutes
Cooling Time 15 minutes
Total Time 30 minutes
Course Breakfast, Snack
Cuisine American
Servings 6 4-oz cups
Calories 128 kcal

Equipment

  • 1 small saucepan
  • 1 wooden spoon
  • 1 potato masher or immersion blender optional
  • 1 medium mixing bowl
  • 6 4-oz sealable glass jars or plastic containers

Ingredients
  

  • 2 ½ cups fresh or frozen fruit
  • 1 tablespoon black or white chia seeds
  • 2 tablespoon honey or maple syrup divided
  • 2 cups plain regular or Greek yogurt

Instructions
 

  • Place the fruit in a small saucepan and cook it on medium heat for 5-10 minutes, stirring regularly, until it has softened and released its juices. If the fruit isn't very "juicy" and you find that it is sticking to the bottom of the saucepan, add a couple tablespoons of water to help break it down.
  • If needed, use a potato masher or immersion blender to break up any large chunks of fruit that haven't broken down during the cooking process. (This step is rarely necessary for berries.) You can also blend the mixture in a blender or food processor for a few seconds before returning it to the saucepan.
  • Add ½ tablespoon of honey, tasting the fruit mixture and adding more honey if needed to remove excess tartness. (Tarter fruit will require more sweetener.) Stir in the chia seeds and cook for 3-5 more minutes on your element's lowest heat setting, stirring frequently. Remove from heat and place in the fridge to cool.
  • While the fruit compote is cooling, pour the yogurt into a bowl and stir in the remaining 1 ½ tablespoons of honey. Taste and adjust the sweetness as needed—the yogurt should only taste slightly sweet, as it will be combined with the fruit compote when eaten.
  • Once the compote has cooled, divide it equally between six sealable 4-ounce mason jars or containers. (You will have about 1 ½ - 2 tablespoons per jar.) Add about ⅓ cup of the sweetened yogurt on top of the fruit compote, dividing it equally between the jars, then place the yogurt cups in the fridge until ready to consume.

Notes

*Nutritional value is an estimate, calculated based on mixed fruit and plain full-fat Greek yogurt.*
1. Ingredient notes: Works well with any fresh or frozen fruit except banana and citrus. If using fresh fruit, prep it by removing stems, pits and large seeds, and chopping large fruit into smaller pieces. Black or white chia seeds will both work, but white seeds are more visually appealing when using light-colored fruit. Vanilla yogurt can be used instead of plain, but it should not be sweetened.
2. Variations & substitutions: To make this recipe lactose-free, use lactose-free yogurt. To make it dairy-free, use plant-based yogurt. To make it vegan, use plant-based yogurt and replace the honey with agave or maple syrup. To increase the protein content, use Greek yogurt and consider sweetening it with protein powder.
3. Storage & serving instructions: Store the sealed yogurt cups in the refrigerator for up to a week. For best results, stir the fruit compote and yogurt together when serving. (You can also add granola, seeds or nuts.)
4. Switching up the flavor: Try different fruit combinations, add citrus zest or add flavored extracts.
5. Helpful tips:
  • Thaw larger frozen fruit (optional): If using larger pieces of frozen fruit rather than berries, thawing them first can help them break down and release their juices.
  • Don't overcook the fruit: Cook the fruit just long enough to allow it to release its juices, but not enough to let them evaporate. Add a bit of water if it is sticking or seems too dry.
  • Don't add too much sweetener: The yogurt should only taste slightly sweet before it is mixed with the fruit.
  • Make the perfect compote: If using an immersion blender, don't over-blend the fruit. Stir a bit of water into the compote if it is too thick or too dry after cooling.

Nutrition

Calories: 128kcalCarbohydrates: 24gProtein: 8gFat: 1gSaturated Fat: 0.1gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 0.1gTrans Fat: 0.01gCholesterol: 3mgSodium: 30mgPotassium: 194mgFiber: 2gSugar: 19gVitamin A: 302IUVitamin C: 2mgCalcium: 92mgIron: 1mg
Have you tried this?Mention @thecunningkitchen or tag #thecunningkitchen to let us know how it went!

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