Seeded Rye Muffins

These seeded rye muffins taste just like a slice of deli rye bread. The aroma while they are baking is so wonderful that you'll think you just walked into a bakery. 

These rye muffins, especially with the included seeds, definitely have the flavor of rye bread but without the work. In fact, if you haven't worked with rye flour, these muffins are a great place to start. 

I enjoyed these muffins warm with butter straight from the oven. They would also be great dipped into a hearty soup such as broccoli cheddar, beef barley, or chicken noodle. I'll definitely be enjoying them all winter long. 

Ingredients:

Bread Flour and Rye Flour: These muffins include a 50/50 mix by volume of bread flour and rye flour. It's very difficult to bake with rye flour all by itself. Adding higher protein bread flour helps strengthen the rye flour. 

For the rye flour, you can use either medium rye or whole rye, also sometimes called dark rye or pumpernickel. Medium rye has some of the bran and germ removed, while whole rye includes the whole rye kernel. 

I used whole rye flour. 

Seeds: I used a combination of caraway, fennel, mustard, anise, and dill seeds. You can use any combination of seeds that you like, but if you want a deli rye flavor, definitely include at least one and a half teaspoons of caraway seeds. Most of the flavor and aroma associated with rye bread is due to caraway seeds. 

Note: Unless you go through seeds pretty quickly, it's a good idea to store them in the freezer. I have so many different ones from trying a variety of recipes and they definitely last a lot longer this way. 

Pantry Ingredients: Baking powder, baking soda, salt, onion powder, dried onions, vegetable oil, and brown sugar (light or dark). 

From the Fridge: Plain yogurt or sour cream, milk, and eggs. I used whole plain yogurt and whole milk. 

To Make These Muffins:

These muffins are super easy to make. You just use the "muffin method," which is combining the dry ingredients in one bowl, the wet ingredients in another, and then mixing the two together. 

Do not over mix the dough or use an electric mixer to mix this batter. Rye has a tendency to become very sticky if it's over handled. 

I used a 1/4 cup cookie scoop (#16) to portion the the batter among the muffin tin cavities. They should be about 3/4 full. 

Before baking the muffins, sprinkle 1/4 teaspoon of the seeds mixture over the tops. 

Recipe Variation:

You can also use this batter to make a quick bread. Bake the batter in an 8 1/2 by 4 1/2 loaf pan for 45 to 50 minutes. It makes a lovely savory loaf. 

More Muffins Using Rye: Apple blueberry rye muffins, ham and cheese rye muffins, cinnamon applesauce and raisin rye muffins, and bacon cheddar muffins. 

Muffin Monday - November 2025! 

Another month, another muffin! 

• Banana Cranberry Muffins from A Day in the Life on the Farm
• Fig Muffins with Creamy Goat Cheese Filling from A Messy Kitchen
• Pumpkin Apple Muffins from Palatable Pastime
• Seeded Rye Muffins from Karen's Kitchen Stories
• Tiny Batch Whole Wheat Blueberry Muffins from Food Lust People Love

#MuffinMonday is a group of muffin loving bakers who get together once a month to bake muffins. You can see all of our lovely muffins by following our Pinterest board. Updated links for all of our past events and more information about Muffin Monday can be found on our home page.

Seeded Rye Muffins

Yield: 12

Author: Karen Kerr

Prep time: 15 MinCook time: 25 MinTotal time: 40 Min

Ingredients

• 120 grams (1 cup) bread flour
• 106 grams (1 cup) medium or whole rye flour
• 2 teaspoons baking powder
• 1/2 teaspoon baking soda
• 1 teaspoon salt
• 1 teaspoon onion powder
• 2 tablespoons mixed seeds (caraway, fennel, mustard, aniseseed, and dill), divided
• 28 grams (2 tablespoons) brown sugar
• 28 grams (1/4 cup) dried chopped onions
• 50 grams (1/4 cup) vegetable oil
• 227 grams (1 cup) plain yogurt or sour cream
• 57 grams (1/4 cup) milk
• 2 large eggs

Instructions

1. Heat your oven to 350 degrees F and line a 12-cavity muffin pan with paper liners or grease the cavities with butter or spray oil.
2. In a large bowl, whisk together the flours, baking powder and soda, onion powder, 1/2 of the seeds, brown sugar, and dried onions.
3. In a medium bowl, whisk together the vegetable oil, yogurt, milk, and eggs. Pour the wet ingredients into the bowl with the dry ingredients and stir until just combined.
4. Using a 1/4 cup cookie scoop, divide the batter among the cavities of the muffin tin. Sprinkle the remaining seeds on top of the muffin batter, 1/4 teaspoon per muffin.
5. Bake the muffins for 20 to 25 minutes, until light golden and a toothpick comes out clean.
6. Turn the muffins out onto a wire rack to cool. Can be served warm or at room temperature.

Nutrition Facts

Calories

158

Fat (grams)

7 g

Sat. Fat (grams)

2 g

Carbs (grams)

20 g

Fiber (grams)

2 g

Net carbs

18 g

Sugar (grams)

4 g

Protein (grams)

5 g

Cholesterol (grams)

34 mg

https://www.karenskitchenstories.com/2025/11/seeded-rye-muffins.html

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Adapted from King Arthur Baking. They have a ton of recipes using rye along with great tips for working with it.