Freeform Rye Muffins with Red Onion & Farmstead Cheese

I feel like it’s been all-carbs, all-the-time around here lately, but I realize that I do this every year around this time: after a summer of free-flowing vegetables from the CSA and farmer’s market, not to mention eating & preserving of all of the season’s fabulous fruits, my body gets to October and suddenly wants meat. And bread. Hearty pastas with cheese and sausage, spicy beans and roasted vegetables. It’s finally cool enough to make keeping the oven on for an hour or two a pleasure, and I wake up to a growling stomach every morning as my body tries to pack on some pounds as proof against the winter cold.

I long ago realized that it’s pointless for me to struggle too much against my body’s food cravings: deprivation is not fun and a losing battle in the end, I believe. Since this is also my favorite weather of the year, I simply make it a point to get out and move more often. Long hikes in the park across the street, bike rides in the woods, climbing at the Gunks (if I’m lucky and Tai & I can manage a day off together). So it becomes a big of chicken-and-egg scenario: am I eating more carbs to fuel the extra exercise, or am I getting more exercise to burn off the extra carbs? Who cares? Either way, I’m eating well and moving well. It all works.

My latest carb attack came on Monday, when I suddently thought of a savory rye muffin recipe that I’ve had tagged for ages in the great Your Organic Kitchen cookbook by Jesse Ziff Cool (I highly recommend this one for unfussy, delicious, seasonal cooking; everything I’ve tried has been no-fail and you can pick up a used copy for a song on Amazon). I’ve had rye flour from Wild Hive in the freezer for ages, just waiting for me to get around to this recipe, and I had picked up some local farmstead cheese at the new DeCicco’s in Cross River (while violently expensive in general, I applaud the decent selection of local cheeses in the gourmet section); buttermilk, an egg and an onion from the farmer’s market last weekend and some fresh thyme from my summer herb pot (which I pulled inside just in time to avoid the big October snowstorm; we’ll see if I can manage to keep it alive over the winter) and in no time at all these savory beauties were browning in the oven, making the kitchen smell fantastic and making my stomach grumble even more.

Hearty rye, crisp sweet onion, tangy cheese: there’s nothing not to love. I think I’ll be making some version of these all winter long. I might need new hiking boots!

Adapted from Rye, Onion, and Swiss Cheese Muffins in Your Organic Kitchen by Jesse Ziff Cool


Freeform Rye Muffins with Red Onion & Farmstead Cheese



  • 4 and 3/4 oz (1 cup) rye flour
  • 4 and 1/2 oz (1 cup) whole wheat pastry flour
  • 1 tbsp baking powder
  • 1/2 tsp salt
  • few grinds black pepper


  • 1 cup buttermilk (or milk, cream, yogurt)
  • 1 large egg
  • 2 tbsp olive oil
  • 1 small red onion, diced (about 1/2 cup)
  • 3 sprigs fresh thyme leaves (about 1/2 tsp packed)
  • 3 oz (about 1 and 1/4 cups) farmstead cheese, grated (I used Harpersfield Jalapeño; the original recipe called for 4 oz/1 cup of Swiss cheese)


  1. Preheat oven to 400 degrees F. Lightly oil a parchment- or Silpat-covered baking sheet.
  2. In a large bowl, whisk together dry ingredients. In a medium bowl, combine wet ingredients, reserving about 1/4 cup of the grated cheese for garnish. Add wet ingredients to dry, folding together just until mixed. Spoon scant quarter-cupfuls onto the baking sheet; top each freeform muffin with a sprinkle of grated cheese. Bake in the preheated oven until lightly browned on top and a cake tester inserted in the middle of a muffin comes out clean, about 20 minutes. Transfer to cooling racks and allow to cool slightly before serving.

Yields 1 dozen muffins.


  1. You can also bake these as a standard muffin in well-oiled muffin tins.
  2. The original recipe called for 2 tbsp of sugar in the dry ingredients: I simply forgot the sugar, but I didn’t miss it. I don’t think it’s necessary.
  3. The thyme did not really come through: next time I would either double it, or omit. The muffins are plenty flavorful without it.
  4. Eat plain, or serve hot with butter or cream cheese, or at room temp as a mini-sandwich bread, stuffed with your favorite sandwich fixings.


At room temperature, covered with a clean kitchen towel, for up to 3 days. As with most muffins, these should freeze well for up to 6 months. Reheat in a 350 degree F oven for 10 – 15 minutes.


Year round, but these seem hearty winter fare to me.


  1. I am wondering if you could overwinter your thyme in a protected spot near the house? I am able to over winter rosemary here in the mid-Atlantic up against the mountains. I have a protected spot right next to the bricks on the house and slightly protected from the wind. I am thinking depending on the variety of thyme, you might be able to try thyme this way.

    And I need to add rye flour to the list to of flours. Would it work with oat flour?

    • I suspect it would get too cold to overwinter thyme outdoors here; maybe with a cloche or other protection, but we do get temps down in the single digits. Right now it seems to be doing fairly well in the house; time will tell what a long dry winter in the house has in store.

      As for oat flour, I’m thinking it might make the muffins too dense; rye is a much coarser grind, typically. You might try 1/2 cup oat flour with 1 and 1/2 cups WW pastry, but I’d sub whole wheat bread flour (hard red wheat) if you can’t find rye. Or something like spelt or triticale would make an interesting sub.

      • Dee G

        I had thyme in a half whiskey barrel in Ulster and it survived every winter from 1990-2010 (I’m no longer there so can’t say whether it lives on.) I didn’t do anything to protect it so it was snow and ice covered at times. In the spring it just bounced back bigger than ever. And if it was a mild winter I picked all season long. This was a classic thyme, not a flavored one. So I think you should be fine even if you left it on a porch or outside. Mine probably benefited from being in such a large pot.

  2. Pingback: A Variety of Quickbreads: Scones, Muffins and Loaves | The Lovely Locavore Ladies of Boston

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