Healthy Savory Breakfast Muffins

Name: Healthy Savory Breakfast Muffins
Prep time: 15 min
Cook time: 25 min
Total time: 40 min
Ingredients: 4 large eggs; 1 cup low-fat cottage cheese; 1/4 cup olive oil; 1 Tbsp maple syrup; 1 ½ cups whole wheat flour; 2 tsp baking powder; 1/2 tsp salt; 3 cups chopped vegetables (broccoli, peppers, corn, spinach, etc); 1 cup cooked ham (chopped (or any lean cooked meat like turkey sausages or chicken)); 1 cup shredded cheddar cheese, divided (or any shredded or crumbled cheese); 1/4 cup chives (or green onions finely sliced)

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by Lily Ernst on October 23, 2025

These healthy savory breakfast muffins are packed with protein, loaded with veggies, and bursting with flavor. Made with ham, eggs, cottage cheese, olive oil, and whole wheat flour – they’re the perfect make-ahead breakfast or snack to fuel your day.

Savory breakfast muffins piled into a pie plate with a blue napkin.

Table of Contents

Why you’ll love this recipe:

High in protein & satisfying – Each muffin is filled with eggs, ham, cottage cheese, and cheddar for a hearty, protein-rich bite that keeps you full and energized.
Loaded with veggies – With three full cups of veggies, these muffins will help you get a healthy start to the day.
Wholesome ingredients – Made with olive oil, whole wheat flour, and a touch of maple syrup for natural sweetness – no refined sugar needed!
Perfect for meal prep – Bake a batch, refrigerate, or freeze, and you’ll have a quick grab-and-go breakfast all week long.

If you are looking for more healthy recipes, try my Healthy Apple Cake, Protein Pumpkin Muffins, and Healthy No-Yeast Cinnamon Rolls.

Savory breakfast muffins on a blue wool napkin in a metal pie pan.

Ingredients you’ll need:

Whole wheat flour – Adds fiber and structure for a hearty, nutritious base.
Baking powder – Helps the muffins rise and stay light and fluffy.
Salt – Enhances flavor and balances the sweetness.
Eggs – Bind the ingredients together and provide protein and moisture.
Cottage cheese – Adds creaminess and extra protein, and keeps the muffins tender.
Olive oil – Contributes healthy fats for moisture and a soft crumb.
Maple syrup – Adds a touch of natural sweetness and helps balance the savory flavors.
Ham – Provides savory flavor and boosts the protein content.
Vegetables – For color, texture, vitamins, and fiber.
Cheddar cheese – Adds a rich, cheesy flavor and extra protein.
Chives – Add a fresh, mild onion flavor that brightens the muffins.

How to make healthy savory breakfast muffins

(The full written and printable recipe is further below.)

Step #1) In a large mixing bowl, whisk together the eggs, cottage cheese, olive oil, and maple syrup.

Step #2) Add the flour, baking powder, and salt. Stir until just combined.

Step #3) Fold in the ham, veggies, chives, and cheese.

Step #4) Divide the batter evenly into a greased muffin pan. Top with remaining cheese. Bake at 375F for 25 minutes.

🌟 Expert tips:

Chop the veggies small so they cook evenly and blend well into the batter.
Use low-fat cottage cheese to reduce calories while keeping the protein high.
Add extra flavor – sprinkle a little everything-bagel seasoning on top before baking or add a little garlic powder or fresh herbs for a fun twist.

Two savory breakfast muffins stacked on a plate with the top one broken in half.

Delicious variations:

✨ Vegetarian version – Skip the ham and add extra veggies or black beans.
🧀 Cheese swap – Try feta, mozzarella, or pepper jack for a new flavor.
🌶️ Spicy kick – Add diced jalapeños or a pinch of chili flakes.
🥓 Meat lovers – Swap the ham for any lean cooked meat, like turkey sausage or chicken.

Storing & freezing instructions:

To store: Keep in an airtight container in the fridge for up to 5 days.
To freeze: Place cooled muffins in a single layer in a freezer bag. Freeze for up to 3 months.
To reheat: Microwave for 30–40 seconds or warm in a toaster oven until heated through.