Fruit on the Bottom Greek Yogurt Snack Cups
High-protein Greek yogurt snack cups with homemade strawberry compote for delicious fruit flavor without additives. Control sweetness, use fresh or frozen berries, and enjoy this make-ahead breakfast or snack all week!

Make these fruit on the bottom yogurt snack cups with clean ingredients that taste better than storebought! As someone who’s always looking for protein-rich snacks that actually taste like a treat, I was tired of grabbing store-bought yogurt cups loaded with mystery ingredients and way too much sugar. After experimenting in my kitchen, I discovered that making homemade fruit on the bottom Greek yogurt snack cups was ridiculously easy ā and so much better!
These cups have become my go-to afternoon snack and my kids’ favorite after-school treat. The concentrated strawberry compote paired with creamy Greek yogurt creates something that tastes indulgent while still packing a serious protein punch. Plus, knowing exactly what’s in them gives me peace of mind I never had with the store versions.
Why You’ll Love This Greek Yogurt Snack Cups Recipe
- High-protein power snack: Each cup delivers a satisfying dose of protein from creamy Greek yogurt, perfect for sustained energy throughout your day.
- Skip the store-bought additives: You control exactly what goes into these cups ā no gums, preservatives, or excessive sugars hiding in the ingredients list.
- Make-ahead convenience: Prep a batch on Sunday and enjoy ready-to-grab snacks all week that travel perfectly to work or school.
- Customizable flavor combinations: While I love the classic strawberry version, this recipe works beautifully with blueberries, raspberries, mangos, or peaches ā mix and match to discover your favorite.

Ingredients & Substitutions
Here is everything you need to make yogurt snack cups with fruit on the bottom:
For the Compote:
Strawberries: Fresh or frozen berries both work perfectly ā I often use frozen when berries aren’t in season. You can swap with blueberries, raspberries, blackberries, peaches, or mangos for endless flavor variations.
Maple Syrup or Honey: Either sweetener works beautifully here ā I prefer honey for flavor but maple syrup also tastes great. Try agave for a vegan option or coconut sugar for a lower glycemic choice.
Lemon Juice: This brightens the fruit flavor and balances sweetness. You can swap with lime juice or orange juice, or skip if using very tart berries.
Vanilla Extract: Adds warmth and rounds out the fruit flavors. Almond extract makes a nice alternative, or try vanilla bean paste for extra vanilla punch.
Salt: Just a pinch enhances all the flavors ā sea salt or kosher salt both work great.
For the Yogurt Cups:
Greek Yogurt: Plain, full-fat Greek yogurt provides the best texture and protein. Try skyr for even more protein, regular yogurt for a lighter option, or coconut yogurt for dairy-free cups.
Honey: A touch of sweetness brings everything together. Swap with maple syrup, agave, or date syrup based on your preference.
Easily Adapt This Recipe for Any Diet
This recipe is naturally easy to tweak! Follow these simple swaps to make it gluten-free, dairy-free, or vegan while keeping the same great texture and flavor.
Gluten-Free: This recipe is naturally gluten-free as written. Just check your vanilla extract label to ensure it’s certified gluten-free if needed.
Dairy-Free: Use coconut yogurt or almond milk yogurt instead of Greek yogurt. Look for unsweetened varieties and adjust honey to taste.
Vegan: Replace Greek yogurt with plant-based yogurt (coconut, almond, or soy) and swap honey for maple syrup or agave nectar.
š” Pro Tip: If you try a substitution, let us know how it worked in the comments!

How to Make My Fruit on the Bottom Greek Yogurt Snack Cups Recipe
Here are easy, detailed, step-by-step instructions that are also repeated in the recipe card at the bottom of this blog post.
Step 1: Cook the Berry Compote
In a medium saucepan, combine the berries, maple syrup, vanilla extract, lemon juice, and pinch of salt.
Cook over medium heat, stirring occasionally with a rubber spatula, until the berries break down, about 5-7 minutes. Mash the berries with a fork or potato masher. Then simmer for an additional 5 minutes or until the sauce thickens to your desired consistency. Remove from heat and set aside to cool.


Step 2: Assemble the Yogurt Cups
In small containers or mason jars, layer 2 tablespoons of the cooled strawberry compote at the bottom. Top with 1/2 cup plain Greek yogurt mixed with 1/2 tablespoon honey. Seal and refrigerate until ready to serve.
Step 3: Store and Serve
These yogurt cups keep well in the refrigerator for up to 5 days. For extra crunch and fiber, top with homemade vanilla almond granola just before serving.

Expert Recipe Tips
Concentrate the flavor: Cooking the fruit compote removes excess water, intensifying the berry flavor far beyond what you get with fresh fruit alone.
Cool completely: Let your compote cool before layering to prevent it from bleeding into the yogurt layer and maintaining those beautiful distinct layers.
Portion control made easy: Using small mason jars or meal prep containers helps with portion control and makes grab-and-go snacking effortless.
Level up with granola: Adding granola just before eating keeps it perfectly crunchy ā try my vanilla almond granola for the ultimate yogurt parfait experience.
Delicious Serving Suggestions
- Portable breakfast option: I like to grab these on busy mornings when I need something quick but satisfying. You’ll love how they keep you full until lunch thanks to the protein-rich Greek yogurt.
- Afternoon energy boost: These make the perfect 3 PM snack when you need a pick-me-up. The natural fruit sugars and protein combo provides sustained energy without the crash.
- Fancy brunch addition: Layer these in clear glasses with vanilla almond granola for an elegant brunch spread. Your guests will never guess how simple they are to make!
- Dessert alternative: With their natural sweetness and creamy texture, these satisfy sweet cravings while still being nutritious. My kids think they’re getting dessert!
Do you love greek yogurt? Check out more of my protein greek yogurt snack recipes:

Fruit on the Bottom Greek Yogurt Snack Cups

Ingredients
Yogurt Fruit Cups
- 1/2 cup greek yogurt
- 1/2 tablespoon honey
- 2 tablespoons strawberry compote
Strawberry Compote:
- 2 cups strawberries (fresh or frozen)
- 2 tablespoons maple syrup
- 1 teaspoon vanilla extract
- 1 teaspoon lemon juice
- 2 pinches salt
Instructions
Strawberry Compote:
- In a medium saucepan, combine the berries, maple syrup, vanilla extract, lemon juice, and pinch of salt.
- Cook over medium heat, stirring occasionally with a rubber spatula, until the berries break down, about 5-7 minutes. Mash the berries with a fork or potato masher. Then simmer for an additional 5 minutes or until the sauce thickens to your desired consistency. Remove from heat and set aside to cool.
Yogurt Cup:
- In small containers or mason jars, layer 2 tablespoons of the cooled strawberry compote at the bottom. Top with 1/2 cup plain Greek yogurt mixed with 1/2 tablespoon honey. Seal and refrigerate until ready to serve.
Video
Notes
Nutrition

This recipe has been reviewed by a healthcare professional for its nutritional balance and alignment with healthy eating principles.
Oh yummm! The fruit sauce is soooo good! These taste like a big kid version of the cups I used to eat when I was little. I can’t wait to try them as a parfait with the granola next time.
Hi Alice, thank you for the review! I love them as parfaits with granola, too š
These yogurt cups are sooo yummy and fun to customize exactly how you like them with clean ingredients š Let me know what you think if you have a chance to make them.