Preheat the oven to 350 degrees Fahrenheit and line a 8” x 8” square baking pan with parchment paper. Note: you can also use a springform pan, 8-inch round cake pan, or a smaller bundt pan if you'd like. If you don't have parchment paper, spray the baking pan with cooking spray.
In a small bowl or measuring cup, stir together the ingredients for the nutty streusel topping until well-combined. Set aside until ready to use.
In a stand mixer fitted with the paddle attachment, cream together the butter and sugar until well-combined and fluffy. Note: you can use a large bowl and an electric hand mixer if you don't have a stand mixer.
Scrape the sides of the bowl and mix in the eggs one at a time on medium speed.
Add in the vanilla extract and Greek yogurt and beat until the wet ingredients are well-combined. Scrape the sides of the bowl.
Stir together the gluten-free all-purpose flour, baking powder, and sea salt (dry ingredients) in a mixing bowl until combined. Leaving the mixer on medium speed, add all of the flour mixture slowly. Beat just until a thick dough forms.
Transfer half of the coffee cake batter to the prepared pan and smooth it into an even layer. The batter will be very thick (this is normal), so don’t worry if this isn’t perfect. I often use my hands to press the dough into a somewhat even layer.
Sprinkle half of the pecan streusel topping over the cake batter and press it gently into the batter.
Spread the remaining cake batter on top, then sprinkle the rest of the streusel topping on top as well. Again, this doesn’t need to be perfect and it is completely fine if your cake layers mix together with your streusel layers.
Bake on the center rack of the preheated oven for 30 minutes. Take the cake out of the oven and carefully cover it with foil (I use two oven mitts to secure the foil over the pan). Bake for another 10 to 15 minutes, or until it tests clean.
You can use a thermometer to check the temperature of the cake. It is done when it reaches 190 to 200 degrees Fahrenheit.
Allow the coffee cake to cool for at least 20 minutes before slicing and serving.