Bacon and Swiss Rye Muffins

These muffins won’t win any beauty contests.  They’re not the prettiest muffins on the block.  They have a muffin face only a mother could love.  But man-oh- man, they’re delicious.  Let me break it down for you…

  1. They have bacon.  That alone should be enough to convince you.
  2. They have Swiss cheese both in them and toasted on top of them.  If the bacon didn’t do it, the Swiss should.
  3. They have rye.  Rye?  Because it’s delicious.  That’s rye.  (Hi, Dad.  Thanks for the line.)

Any of those ingredients alone would be enough to make me dive mouth first into a muffin, but putting them together?  Oh my.  Oh me.  It’s enough to drive a girl crazy with food lust.  The salty, smoky bacon, pungent Swiss cheese (nothing neutral here) and sharp Rye flavors are all enhanced by a subtle presence of onion.  It’s the ultimate deli experience encapsulated in one lovely (in a ugly duckling to swan sort of way) muffin.

Get in my belly!

What can you serve with these muffins?  Soup, salad, or nothing at all.  While they make a wonderful companion to creamy and brothy soups, or dinner salads, they stand alone as a hearty snack or breakfast, too.  They store well, wrapped, in the refrigerator and I would imagine they freeze well, too.  There is a disclaimer, though; we’ve never had a batch last long enough to freeze.  Mainly they vaporize within a day.

In the interest of science, though, I wrapped and hid three muffins in the back of the refrigerator for four days.  Okay, the truth is I put three muffins in the fridge and ate one the next day.  On the second day I ate another one.  On the third day, my son broke his arm.  On the fourth day, I ate that last one.  It was still marvelous.  It was, as I said, a highly scientific process.

One more look before we make them?  Certainly.

For a printer friendly, photo-free version of this recipe, click here!

Bacon and Swiss Rye Muffins

Adapted from King Arthur Flour’s Ham-and-Cheese Rye Muffins


  • 2 cups (7 1/2 ounces) whole rye flour (also known as pumpernickel flour)
  • 3/4 cup (3 1/8 ounces) high-gluten flour (also known as bread flour)
  • 2 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1 teaspoon Kosher salt
  • 3/4 teaspoon granulated onion
  • 1 1/2 cups Swiss cheese, grated and divided
  • 1 large egg
  • 1 1/2 cups (12 fluid ounces) buttermilk (or 1 1/2 teaspoons cider vinegar in a measuring cup topped with enough milk to reach 1 1/2 cups)
  • 1/2 cup (4 ounces by weight) melted unsalted butter
  • 1/2 pound of bacon, sliced into thin strips and then cooked until crispy and drained on paper towels

Preheat the oven to 375°F.

Generously grease a muffin tin or line with papers that are sprayed with non-stick cooking spray.  This may seem like overkill, but the cheese likes to stick.  Greasing the papers or the tins will ensure that you don’t have to gnaw crispy cheese bits from paper or a pan.  I’ve done it.  Trust me.  In a big mixing bowl, whisk together the rye flour, high-gluten flour,  baking powder and soda, salt and granulated onion.  Toss in 1 1/4 cups of the grated Swiss cheese to ensure it’s coated with flour.

Whisk together the egg, buttermilk and melted butter in a separate bowl or large measuring cup.  Pour into the flour mixture all at once and stir until it is evenly moist.  Do not overmix.  Gently stir in the crisp bacon.

Scoop the batter into the prepared pan.  Since whole grain muffins do not rise as much as their non-whole grain counterparts, you can fill these tins or papers fairly full.  You should get 12 muffins out of this batter.

Evenly divide the remaining 1/4 cup of Swiss cheese between the tops of the muffins and put the pan in the oven.  Bake 25 minutes or until the cheese on top is toasty and deep golden brown and the muffins test done.  (To test muffins, insert a skewer or toothpick into the center.  If it comes out clean- with perhaps a little oil from the cheese or bacon but no clumps of batter- the muffins are done.)

Allow the muffins to cool in the pan for 5 minutes then turn them out on a rack to continue cooling.  Or just eliminate that step and eat them immediately.  I won’t tell.


  1. Ann H says

    Anything draped in melted Swiss is to be considered beautiful! Furthermore, these sound delish! I prefer a savory muffin. I would not think to use the high gluten flour in a muffin. I’m definitely going to give these a try.

    • Rebecca says

      Ann- You make a good point about foods draped in Swiss cheese. And they are delicious. You also raise a good point about the high gluten flour. Because this recipe uses the whole rye (pumpernickel) flour, the high-gluten flour provides some lift to the final product. Because the gluten in rye isn’t particularly strong it needs a little boost for which the high-gluten flour is well suited. The extra gluten helps hold the gas in from the leavening process creating a lighter end product. And that is probably way more than you cared to hear. Sorry.

  2. says

    These look great-your photos are wonderful. And I think its great that in the name of science you made the 4 day freshness taste (test). Hope your son’s arm is on the mend-I can see why you needed to skip a day. Thanks for sharing one of King Arthur Flour’s recipe. Joan D@bakershotline

  3. Annette says

    I love you , umm sorry I love your savory muffins. I think these could be my new best friends. I have to bake a batch and see how compatible we are, something tells me were going to get along just wonderfully. What a wonderful brunch dish, great for parties, picnics, womens luncheons and late night visits to the kitchen. Your recipe is so well written I should have no problem making these and believe me I need specific well detail recipes. Thank you so much.

  4. Lisa says

    I tried the ham and swiss combo, and though they were really good, the thin deli ham I used got lost in these muffins. I would try cubes of a good smoked ham, and definitely try the bacon! Yah, anything with bacon! Great muffins, thanks.

  5. Annette says

    I made these tonight. Mine are as pretty as yours. They sorta looked dry and when tasted they were very dry. I think 25 minutes might have been long, but my cheese didnt really brown at all. I was so looking forward to these and after 2 weeks of major rye flour hunting, requiring ordering online finally, I think I have to tweak this some. The 25 min is long for a muffin, more cheese and more bacon perhaps, I just not sure, but it needed moisture. I told my friend maybe slather some mayonaise or something on it, were still looking for a save somehow.

  6. Gwen in L.A. says

    These are addictive. I grind my own rye flour btw. Since bacon has been ruled out of my diet I’ve made them with the Swiss cheese only, and a couple of times added toasted sunflower kernals.

    Still addicting, years later. I order whole grain rye from Honeyville just to make these LOL


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