Preheat oven to 375. Line a 12-cup muffin tin with muffin cups.
Peel, core, and roughly chop the apples. Puree them by placing in a food processor and blending until the consistency of apple sauce is achieved (Don't completely liquefy).
In a large bowl, place flour, flaxseed, baking powder, cinnamon, and salt, and stir to combine.
Add the raisins and apple puree, and mix with a wooden spoon to combine.
Stir in the lemon juice, zest, honey, and almond milk, and mix just until incorporated. The batter should be thick, but if it seems overly dry, you can stir in more almond milk until the mixture is moist.
Spoon the batter into the muffin cups. Bake until golden and a tooth pick inserted in the center of a muffin comes out clean, around 30 minutes.
Place muffins on a wire rack to cool before enjoying.