Macaroni and Cheese Cups

What Kind of Mac and Cheese Works Best?

While just about any leftover mac and cheese can work, a thicker, creamier version is ideal. It holds together better during baking and delivers that rich, cheesy bite in every bite.

• Homemade macaroni: I love using my creamy, one-pot mac and cheese recipe. It has the perfect sauce-to-pasta ratio and a rich flavor that helps the muffin cups hold their shape while staying soft and cheesy inside.
• Boxed (like Kraft): Short on time? Boxed variety is a great shortcut. Just make sure it’s thick and creamy enough to scoop easily—avoid overly saucy versions.
• Baked Casserole : This version tends to be denser, so it’s not the best fit. But if it’s what you have, just stir in a splash of milk or a bit more shredded cheese to loosen it up before shaping.

Tip: Let your macaroni cool to room temperature before forming into cups—this helps them hold together better in the muffin pan.

Types of cheese to use

For best results, stick with the same cheese used in your macaroni recipe so the flavor stays cohesive. In my homemade recipe, I use sharp cheddar for its bold, classic taste. If you're working with boxed versions like Kraft, you can easily enhance it by mixing in a handful of shredded cheeses—try gruyère for a nutty note, gouda or Monterey Jack for creaminess, or even Swiss. Combining a few cheeses adds depth, making the cups even more flavorful.

Can you use paper liners for macaroni and cheese cups?

It’s best to skip the paper liners and grease the muffin pan instead—this gives the baked muffin bites a crisp, golden crust around the edges that you just can’t get with liners. However, if you do opt for paper liners for easier cleanup, make sure to let the cupcakes cool completely before removing them, as this helps prevent sticking and keeps them from falling apart.

Step 7 - Bake at 425 degrees for 20 to 25 minutes or the tops are deep golden and crisp.

Looking for more ways to use leftover mac and cheese?

While I’m a big fan of these muffins, there are plenty of other creative ways to use your leftover pasta, as shared by fellow bloggers:

• Waffles - Spread leftovers into a waffle maker and cook until crispy for a fun, savory snack.
• Balls - Shape into balls, coat with breadcrumbs, and fry, bake or air fry for a crunchy snack or appetizer.
• Soup - Thin the leftovers with a little milk or broth, then add extra seasonings to turn it into a creamy soup.
• Frittata - Mix with eggs and veggies, then bake for a savory frittata.
• Stuffed peppers - Fill red or green bell peppers with leftovers, top with cheese, and bake until golden and bubbly.

Sucess tips

• Grease the muffin pan generously, as these bites tend to stick. A good coating will ensure they release easily once baked.
• To remove the muffins from the pan, run a knife around the edges to loosen them before lifting them out. If using paper liners, gently peel them away to release the muffins.
• For best results, use pasta at room temperature. Cold macaroni can be too stiff and difficult to incorporate with the other ingredients.

Storage and Reheating Instructions

To store: Store the cups in the fridge for 3 to 5 days, or freeze in a sealed zip-top bag for up to one month.

To reheat: Bake the frozen cups in a preheated 350°F oven for 15-20 minutes, or air fry at the same temperature for 8-10 minutes. For a quicker option, you can microwave them for 1-2 minutes, though this will result in a less crispy texture.