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May 26, 2024

Ham and Cheese Rye Muffins

These Ham and Cheese Rye Muffins are a wonderful take on the ham and cheese on rye sandwich. They are also a great portable breakfast. 

Ham and Cheese Rye Muffins with a muffin on an individual plate.

These ham and cheese rye muffins are made with whole grain rye flour, bread flour, as well as ham and cheese. 

They also contain a bit of onion powder, which adds to the savory flavor. Add some grated cheese on top and you have the perfect quick and savory breakfast. Plus, there is no sugar added to the batter. 

Ham and Cheese Rye Muffins on a black mini plate.

The first time I made these I took them to work. Let's just say, these didn't last very long at all! 

What does the rye in these muffins taste like?

Forget what you think about the taste of rye. What most people think of as rye flavor is actually the flavor of the caraway seeds that are typically in deli rye bread. In reality, the flavor of rye flour is very mild, and actually much milder than whole wheat. 

The flavor is kind of earthy, but not particularly strong even though it is the whole grain version. 

Ham and Cheese Rye Muffins on a white tray.

Ingredients in these ham and cheese rye muffins:

Rye Flour: I used whole rye flour, also known as pumpernickel flour or dark rye flour. It contains all of the germ, bran, and nutrition of the whole rye berry. 

Diced Ham: While I made these muffins with ham, they can also be made with cooked bacon for an extra rich treat. 

Shredded Cheese: I've made these with Swiss or Gruyère cheese, sometimes supplemented with a little bit of cheddar to top the muffins. 

Buttermilk: You can use either whole buttermilk or powdered buttermilk. If you use powdered buttermilk, mix the dry powder into the flour mixture and add the equivalent water to the wet ingredients. 

From the Pantry and Fridge: Bread flour, baking powder, baking soda, salt, onion powder, butter, and egg. 

Ham and Cheese Rye Muffins on a green plate.

Tips for Making these Ham and Cheese Rye Muffins: 

Working with rye flour can be a challenge. You should not overwork the batter because it can get gummy if you are not careful. Mix the batter just until it comes together, and don't worry too much if there are bits of flour that have not been fully incorporated. Once the muffins start baking, rest assured, the bits of flour will disappear. 

Be sure to use bread flour instead of all purpose flour for the white flour. The extra protein gives the dough some strength. 

Because of the cheese in the batter, the muffins can stick to either the the muffin tin or the muffin papers, be sure to grease the pan or spray the paper liner with spray oil. You can also use nonstick muffin paper liners. My favorite brand is PaperChef. They don't seem to stick to anything!

Ham and Cheese Rye Muffins with two different cheeses on top.

I've made these both with and without paper liners. Without the paper liners, this recipe yields about 12 muffins, and with the paper liners, the recipe yields about 15 muffins (the paper takes up some space). 

I made these with Gruyère cheese this time, and blended in some cheddar on top of a few. 

These muffins are delicious served warm. Leftovers can be re-warmed for about 15 to 20 seconds in the microwave.

If You Love Ham and Cheese, Here are More Recipes:

Sous Vide Ham and Cheese Egg Bites

Spinach, Ham, and Cheese Puff Pastry Bites

Ham and Cheese Breakfast Casserole

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Welcome to this month's Muffin Monday! 

#MuffinMonday is a group of muffin loving bakers who get together once a month to bake muffins to brighten their Mondays. You can see all our of lovely muffins by following our Pinterest board.

Ham and Cheese Rye Muffins on a white tray.

Ham and Cheese Rye Muffins

Ham and Cheese Rye Muffins
Yield: 15 muffins
Author: Karen's Kitchen Stories
Prep time: 20 MinCook time: 25 MinTotal time: 45 Min
These Ham and Cheese Rye Muffins are a wonderful take on the ham and cheese on rye sandwich. They are also a great portable breakfast.


  • 213 grams (7 1/2 ounces/2 cups) whole rye flour
  • 88 grams (3⅛ ounces/ 3/4 cup) unbleached bread flour
  • 2½ teaspoons baking powder
  • ½ teaspoon baking soda
  • 1 teaspoon salt
  • 1/2 teaspoon onion powder or granulated onion
  • 6 ounces (1 1/2 cups) grated cheese (Swiss, Gruyère, or cheddar, or a combination)
  • 1 large egg, room temperature
  • 1 1/2 cups buttermilk
  • 1 stick (4 ounces/ 1/2 cup) unsalted butter, melted
  • 4 ounces diced ham


  1. Preheat the oven to 375 degrees F and fill the cavities of muffin tins with 15 paper liners. Spray the paper liners lightly with with spray oil.
  2. In a medium bowl, whisk together the dry ingredients.
  3. Add all but ¼ Cup of the Swiss cheese and toss to coat the individual pieces of cheese.
  4. In another bowl, mix the egg, buttermilk, and the butter. Pour it into the flour mixture and stir until just incorporated.
  5. Add the ham and stir until evenly distributed.
  6. Using an ice cream scoop, portion the batter into the muffin cavities, and top each with some of the reserved cheese.
  7. Bake for 25 to 27 minutes, one muffin tin at a time, until a toothpick comes out clean.
  8. Cool in the pan for 5 minutes.
  9. Remove from the pan and cool on a rack…. or eat while still warm!

Nutrition Facts



Fat (grams)

12 g

Sat. Fat (grams)

7 g

Carbs (grams)

17 g

Fiber (grams)

2 g

Net carbs

15 g

Sugar (grams)

2 g

Protein (grams)

7 g

Cholesterol (grams)

47 mg
rye, ham, breakfast
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Recipe adapted from Whole Grain Baking: Delicious Recipes Using Nutritious Whole Grains (2009). 

Would you like to comment?

  1. Ham and cheese is such a classic combo! I love that you used rye flour, Karen!


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