Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease with cooking spray.
In a large bowl, mix together the whole wheat pastry flour, baking powder, baking soda, cinnamon, and salt until well combined.
In a separate bowl, combine the unsweetened applesauce, mashed ripe banana, almond milk, melted coconut oil, and vanilla extract. Mix until smooth.
Pour the wet ingredients into the dry ingredients and gently fold together until just combined, being careful not to overmix.
Gently fold in the blueberries or raspberries, chopped nuts, sugar-free chocolate chips, and lemon zest until evenly distributed.
Divide the batter evenly among the prepared muffin cups, filling each about ¾ full.
Bake in the preheated oven for 18-20 minutes, or until the muffins are golden and a toothpick inserted into the center comes out clean.
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.