Air Fryer Egg Muffins (Keto Mini Cheese Frittatas)

Air fryer egg muffins are the easiest keto breakfast you’ll make all week — just 5 ingredients, one bowl, and 15 minutes from start to plate. Think of them as mini cheese frittatas baked right in a muffin tin: fluffy, cheesy, and endlessly customizable. At roughly 1 gram of net carb each, they’re a genuine low-carb win, and because they reheat beautifully, they’re perfect for meal prep and grab-and-go mornings.

I make a batch almost every Sunday. They stock the fridge for busy weekdays, they freeze like a dream, and they’re the base recipe I riff on constantly — swap the cheese, throw in leftover veggies, add crumbled bacon, and you’ve got a brand-new breakfast. If you love a good egg recipe in the air fryer, this one earns a permanent spot in the rotation.

Looking for more easy egg ideas? A few reader favorites are my air fryer scrambled eggs, air fryer hard boiled eggs, and these low-carb air fryer scotch eggs.

Why You’ll Love These Air Fryer Egg Muffins

• 5 simple ingredients you almost certainly already have on hand.
• Keto and low-carb friendly — about 1g net carb per muffin, with the protein to keep you full.
• Ready in 15 minutes, start to finish, with almost no hands-on time.
• Meal-prep and freezer friendly — make a big batch and reheat all week.
• Totally customizable — the plain cheese version is just the starting point.

Ingredients Needed

Here’s everything you need for a batch of mini cheese frittatas:

• Eggs — 4 large eggs form the base.
• Milk or heavy cream — a splash keeps them tender. Use heavy cream to stay strictly keto.
• Shredded cheddar cheese — or any melting cheese you love (see variations below).
• Salt — to taste.
• Black pepper — to taste.

That’s it. The magic of this recipe is how forgiving it is, so don’t stress about exact amounts.

How to Make Egg Muffins in the Air Fryer

Step 1: Grease your muffin tin well. Brush the cups with olive oil or hit them with non-stick cooking spray, getting into every corner so the muffins pop out cleanly. Silicone muffin cups work great here too — just grease those as well.

Step 2: Whisk the eggs. Crack the eggs into a bowl, then add the milk (or heavy cream), salt, pepper, and shredded cheese. Whisk until everything is well combined and a little frothy.

Step 3: Fill the cups two-thirds full. The egg muffins puff up as they cook, so leaving headroom keeps them from overflowing.

Step 4: Air fry at 350°F for about 5 minutes. Set the muffin tin into the air fryer basket and cook until the centers are set and no longer jiggly. Cook time can vary by a minute or two depending on your machine.

Step 5: Cool slightly, then release. Let the frittatas rest a few minutes before running a knife around the edges and popping them out

Pro Tips for Perfect Mini Frittatas

• Grease more than you think you need to. Eggs are notorious stickers — a well-oiled tin (or silicone cups) is the difference between clean release and a scrambled mess.
• Don’t overfill. Two-thirds full is the sweet spot; they rise as they cook.
• Let them cool before removing. Warm frittatas are fragile and will tear if you rush them out of the pan.
• Every air fryer is different. This recipe works in any model — including the Ninja Foodi, Instant Pot Vortex, Instant Pot Crisp Lid, and Mealthy lid — but temperature and time may shift slightly, so check for a set center the first time.

Variations and Add-Ins

The plain cheese version is your blank canvas. Fill the cups a little less than two-thirds so you have room for mix-ins, then try:

• Meat lovers: crumbled cooked bacon, diced ham, or breakfast sausage. If you love a bacon-and-egg combo, you’ll also love these air fryer bacon and egg cups.
• Veggie: spinach, diced bell pepper, mushrooms, or chopped tomato (pat wet veggies dry first).
• Ham and cheese: a classic — see my dedicated air fryer ham and egg cups for that version.
• Cheese swaps: pepper jack for heat, feta for tang, Swiss or gruyère for a nuttier frittata.
• Herbs: fresh chives, parsley, or a pinch of everything bagel seasoning.

For even more ideas, this roundup of genius ways to use egg molds in your air fryer is a fun rabbit hole.

How to Store Egg Muffins

These are made for meal prep. Let the frittatas cool to room temperature, then transfer them to an airtight container in the refrigerator, where they’ll keep for 3 to 4 days. Reheat in the air fryer or microwave until warmed through.

How to Freeze Breakfast Egg Muffins

To freeze, cool the muffins completely, then place them in a freezer-safe container or bag. They’ll last 1 to 2 months. Reheat straight from frozen, or thaw overnight in the fridge and warm them in the microwave or air fryer. They’re a lifesaver on hectic mornings — pair a couple with an air fryer loaded breakfast burrito on days you need something heartier.

Frequently Asked Questions

Are air fryer egg muffins keto? Yes. At about 1g net carb each, these mini cheese frittatas fit comfortably into a keto or low-carb diet. Use heavy cream instead of milk to keep the carb count at its lowest.

Why did my egg muffins stick to the pan? Almost always under-greasing. Coat the muffin cups generously with oil or non-stick spray, or use silicone cups, and let the muffins cool a few minutes before releasing them.

Can I make these ahead for the week? Absolutely — that’s the whole point. They keep 3 to 4 days in the fridge and 1 to 2 months in the freezer, and reheat in about a minute.

What air fryers work for this recipe? Any of them. Basket-style and oven-style air fryers both work, as do multi-cookers with an air fryer or crisp lid. Just watch the center the first time to dial in your machine’s timing.

Can I use a different cheese? Definitely. Cheddar is the default, but pepper jack, Swiss, gruyère, and feta all work beautifully.

More Air Fryer Breakfast Recipes You’ll Love

• Air Fryer Avocado Toast with Egg
• Air Fryer Copycat McDonald’s Egg McMuffin
• Air Fryer Ham and Egg Cups
• Air Fryer Bacon and Egg Cups (Keto)

Want a full week of low-carb mornings mapped out? My weekly meal plan and the rest of my breakfast recipes are a great place to start.