Preheat the oven to 350℉ and grease and line a 9-inch springform pan with a circle of parchment paper.
In a medium bowl, whisk together the 1 ½ cups whole wheat flour, ½ cup almond flour, 2 teaspoons baking powder, ½ teaspoon fine sea salt, and ½ teaspoon ground ginger.
In a large bowl, cream the ¾ cup unsalted butter and 1 cup granulated sugar until light and fluffy, about 2 minutes. Add the 3 large eggs one at a time, beating well to incorporate, then beat in the 1 teaspoon pure vanilla extract
Beat in one-half of the flour mixture, then the ½ cup plain yogurt, then the remaining flour mixture, beating until smooth. Scrape down the bowl. Fold in the 1 cup chopped rhubarb and chopped 1 apple until evenly distributed. Spread the batter into the prepared pan and smooth the top with a rubber spatula.
Place in the oven and bake for up to 1 hour, checking around 50 minutes, until lightly golden and a tester inserted in the center comes out clean. Remove and place on a wire rack to cool for 20 minutes, then gently remove from the pan to finish cooling completely. Dust with powdered sugar for serving if desired.
Notes
It has a long bake time. You'll note the hour-long bake time. Not to worry - this is expected because of the fruit, which has a high water content, thus the need to extend the baking time.
Use all-purpose flour. You can use all-purpose flour here instead of whole grain flour, and you can also omit the almond flour if you don't eat nuts. Use 2 cups of all-purpose flour instead of the mix of whole wheat and almond flour, or 1 ½ cups of all-purpose flour for the whole wheat flour.
Add another fruit. Try adding another seasonal fruit to the mix, such as ½ cup of raspberries or blueberries.
Dairy-free: Swap the butter for non-dairy butter and the yogurt for non-dairy yogurt.
What size pan? I like to use a 9-inch springform pan to bake this cake because it's a bit of a taller cake, but you can also use a 9x13-inch pan for a thinner cake, similar to my gluten free strawberry rhubarb cake structure.
To finish: Powdered sugar is my favorite and easiest way to serve this cake. Just sift a bit over the top after it's cooled. You could also add a lemon glaze. I like slices plain, or served with whipped cream or a scoop of ice cream.