These mini muffins are the kind of snack that disappears fast. They’re savory, packed with protein, and easy to eat on the go. Whether you need a quick breakfast, a gym bag bite, or something kid-friendly, these fit the bill.

They bake up in one bowl, freeze well, and taste great warm or cold. Keep a batch in the fridge and thank yourself all week.

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What Makes This Special

Overhead shot of freshly baked Mini Ham & Cheese Protein Muffins cooling in a 24-cup mini muffin tin

Protein-forward and satisfying: Each mini muffin delivers a solid bite of protein without feeling heavy.
One-bowl simplicity: Minimal mess, quick prep, and fast cleanup.
Customizable: Swap the cheese, change the herbs, or switch the meat. It’s flexible.
Kid-approved: Familiar flavors, small size, and soft texture make these easy winners.
Perfect for meal prep: Store well and reheat beautifully.

Ingredients

6 large eggs
1/2 cup plain Greek yogurt (2% or whole milk)
1/2 cup cottage cheese (small curd), blended or whisked smooth
1 cup finely diced cooked ham
3/4 cup shredded sharp cheddar (or Swiss/Gruyère)
1/4 cup finely chopped green onions (or chives)
1/3 cup almond flour or oat flour (for structure)
1 teaspoon baking powder
1 teaspoon Dijon mustard
1/2 teaspoon garlic powder
1/2 teaspoon onion powder
1/4 teaspoon black pepper
1/4 teaspoon salt (adjust based on saltiness of ham and cheese)
Optional: pinch of red pepper flakes or smoked paprika
Olive oil spray or butter for greasing the pan

How to Make It

Close-up, of a plated final serving: three Mini Ham & Cheese Protein Muffins on a matte white plate

Prep the pan: Heat the oven to 350°F (175°C).
Grease a 24-cup mini muffin tin well, or use mini liners.
Whisk the base: In a large bowl, whisk eggs, Greek yogurt, cottage cheese, and Dijon until smooth.
Add dry ingredients: Stir in almond or oat flour, baking powder, garlic powder, onion powder, pepper, and salt.
Fold in the good stuff: Mix in ham, cheddar, and green onions. Batter will be pourable but thick.
Fill the cups: Divide evenly among muffin cups, filling each about 90% full. Top with a sprinkle of cheese if you like.
Bake: Bake 12–15 minutes, until set in the center and lightly golden at the edges.
A toothpick should come out mostly clean.
Cool: Let rest in the pan 5 minutes, then loosen edges and transfer to a rack. They’ll firm up as they cool.
Serve or store: Enjoy warm, or cool completely before refrigerating or freezing.

Keeping It Fresh

Refrigerate: Store in an airtight container for up to 4 days. Place a paper towel in the container to absorb moisture.
Freeze: Freeze in a single layer, then move to a freezer bag.
Keeps well for 2–3 months.
Reheat: Microwave 20–30 seconds per muffin from the fridge, 45–60 seconds from frozen. Or warm in a 325°F oven for 8–10 minutes.

Benefits of This Recipe

High in protein: Eggs, ham, and dairy deliver staying power without excess carbs.
Low effort, big payoff: Simple ingredients and quick bake time.
Portable: Easy to pack for work, school, or travel days.
Balanced: A mix of protein, fat, and a touch of carbs for steady energy.

What Not to Do

Don’t skip greasing the pan: These can stick. Even with nonstick pans, use spray or liners.
Don’t overbake: Dry, rubbery muffins happen fast.
Pull them as soon as the centers are set.
Don’t overload with watery veggies: If adding veggies, sauté and drain first to avoid soggy muffins.
Don’t add too much salt: Ham and cheese are already salty. Taste the batter if you’re unsure.

Variations You Can Try

Turkey and Swiss: Swap ham for turkey and cheddar for Swiss. Add a pinch of thyme.
Bacon and Gouda: Use crisp bacon pieces and smoked Gouda for a deeper flavor.
Veggie Boost: Fold in sautéed spinach, bell peppers, or mushrooms.
Pat dry before adding.
Spicy Kick: Add jalapeños and pepper jack, plus a dash of hot sauce.
Gluten-free or grain-free: Stick with almond flour, or use a tablespoon of coconut flour (very absorbent—don’t add more).

FAQ

Can I make these in a regular muffin tin?

Yes. Bake at the same temperature for about 18–22 minutes. Fill cups nearly to the top and check for set centers.

Do I have to use cottage cheese?

No.

You can replace it with more Greek yogurt, though cottage cheese adds great texture and extra protein.

Can I use egg whites only?

You can, but the muffins will be less rich and may be drier. Use about 10 egg whites and add an extra tablespoon of olive oil or melted butter for moisture.

What cheese works best?

Cheddar, Swiss, Gruyère, Monterey Jack, or a blend all melt well. Choose something with good flavor so you don’t need much.

How do I prevent sticking?

Grease generously, run a thin knife around the edges after baking, and let them rest 5 minutes before removing.

Are these good cold?

Yes.

They’re tasty straight from the fridge and make a great quick snack or lunchbox add-on.

Can I double the recipe?

Absolutely. Use two pans or bake in batches. Whisk the batter again before filling the second pan to keep ingredients evenly distributed.

Final Thoughts

Mini Ham & Cheese Protein Muffins are the kind of meal prep that makes life easier.

They’re quick to mix, fast to bake, and built to keep you full. Keep a stash ready for busy mornings, after-school snacks, or post-workout fuel. Simple, savory, and dependable—just how a go-to recipe should be.