Preheat oven to 350°F. Lightly spray or line with cupcake liners 12 muffin tin cups. Set aside.
Spray the inside of medium sized sauté pan with canola oil and heat over medium high heat.
Once hot, sauté the fennel until soft and slightly caramelized, about 5-7 minutes. Allow the mixture to cool completely, set aside until ready to use.
In a mixer fitted with a paddle attachment, cream the canned pumpkin on medium-high speed until smooth, 1-2 minutes. Once smooth, add the butter and sugars and cream again for an additional 1-2 minutes. Turn the mixer off and use a spatula to scrape the sides of the mixer bowl.
On low speed, add the egg and continue to mix for an additional 30 seconds to a minute until fully incorporated. Turn the mixer off and use a spatula to scrape the sides of the mixer bowl. Remove mixer bowl from stand.
In a medium bowl, whisk together the spices, salt, flour, baking powder, baking soda and whole wheat flour.
In the mixer bowl, combine the wet and the dry ingredients together just incorporated. Stir in the caramelized fennel, orange zest and cooked red quinoa.
Using a 1-1/2 oz. portion scoop or a tablespoon measure, scoop the batter into the prepared muffin tins. Sprinkle the tops of the muffins with the pumpkin seeds. Bake in preheated oven until the batter has risen and a tooth pick inserted comes out clean, about 18-23 minutes.
Allow the muffins to cool completely before serving, serving size is 1 muffin.