Run pineapple and carrots through juicer according to manufacturer's instructions. Pour juice into a container and reserve pulp in a bowl. Run zucchini through juicer and add zucchini pulp to pineapple-carrot pulp. Discard zucchini juice.
Measure 2 cups pineapple-carrot juice. If juice doesn't reach 2 cups, add enough water to make 2 cups. Bring pineapple-carrot juice and quinoa to a boil in a saucepan. Reduce heat to medium-low, cover, and simmer until quinoa is tender and liquid has been absorbed, 15 to 20 minutes. Measure 1 cup cooked quinoa and set aside to cool.
Preheat oven to 350 degrees F (175 degrees C). Grease 16 silicon muffin cup molds and place on a baking sheet or line a muffin tin with paper liners.
Sift whole wheat flour, all-purpose flour, cinnamon, baking soda, baking powder, salt, and nutmeg together in a bowl.
Mix applesauce, yogurt, sugar, eggs, coconut oil, and vanilla extract together in a bowl. Stir applesauce mixture, small amounts at a time, into flour mixture until batter is just combined. Fold the reserved 1 cup cooked quinoa, hempseed, raisins, and pineapple-carrot-zucchini pulp into batter; allow to sit for 5 to 10 minutes.
Spoon a heaping 1/3 cup batter into each muffin cup.
Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, 23 to 27 minutes. Cool muffins in tin for 5 minutes before removing from muffin cups.
