Pumpkin Cheesecake Muffins

Loaded with pumpkin seeds, canned pumpkin purée, and pumpkin pie spice, these big streusel-topped muffins are every fall lover’s dream come true. And to make things even better, the inside of each muffin is stuffed with a soft, lightly sweetened cream cheese mixture. Make the cheesecake filling and the streusel ahead of time to pace things out if it’s helpful. Don’t, even for a minute, consider using anything other than Libby’s 100% pure pumpkin purée (not pie mix). Nothing is better. We promise.This recipe is part of Pumpkin Week 2026, Bon Appétit’s annual celebration of autumn’s most magical pantry staple.Recipe informationIngredientsStreusel⅓cup coarsely chopped raw pumpkin seeds¼cup (31 g) all-purpose flour2Tbsp. light brown sugar½tsp. pumpkin pie spiceKosher salt2Tbsp. unsalted butter, room temperatureFilling6oz. cream cheese, room temperature¼cup (50 g) granulated sugar2tsp. all-purpose flour2tsp. vanilla extract½tsp. Diamond Crystal or ¼ tsp. Morton kosher saltBatter and Assembly2large eggs1½cups (packed; 300 g) light brown sugar1cup canned pumpkin purée¼cup extra-virgin olive oil4Tbsp. unsalted butter, melted, slightly cooled¼cup whole milk1Tbsp. pumpkin pie spice1Tbsp. vanilla bean paste or vanilla extract1½tsp. Diamond Crystal or 1 tsp. Morton kosher salt1¾cups (219 g) all-purpose flour1½tsp. baking powderVegetable oil or nonstick vegetable oil spray (for ice cream scoop)Special Equipment12paper linersNeed to make a substitution?PreparationStreuselStep 1Place a rack in middle of oven; preheat to 375°. Line cups of a standard 12-cup muffin pan with paper liners. Whisk ⅓ cup coarsely chopped raw pumpkin seeds, ¼ cup (31 g) all-purpose flour, 2 Tbsp. light brown sugar, ½ tsp. pumpkin pie spice, and a pinch of kosher salt in a small bowl to combine. Using your fingers, rub in 2 Tbsp. unsalted butter, room temperature, until moist pea-size lumps form. Chill until ready to use.Do Ahead: Streusel can be made 1 day ahead. Cover and keep chilled.FillingStep 2Vigorously whisk 6 oz. cream cheese, room temperature, ¼ cup (50 g) granulated sugar, 2 tsp. all-purpose flour, 2 tsp. vanilla extract, and ½ tsp. Diamond Crystal or ¼ tsp. Morton kosher salt in a medium bowl until combined and smooth.Do Ahead: Filling can be made 1 day ahead. Cover and chill.Batter and AssemblyStep 3Whisk 2 large eggs, 1½ cups (packed; 300 g) light brown sugar, 1 cup canned pumpkin purée, ¼ cup extra-virgin olive oil, 4 Tbsp. unsalted butter, melted, slightly cooled, ¼ cup whole milk, 1 Tbsp. pumpkin pie spice, 1 Tbsp. vanilla bean paste or vanilla extract, and 1½ tsp. Diamond Crystal or 1 tsp. Morton kosher salt in a large bowl until smooth, about 1 minute. Whisk 1¾ cups (219 g) all-purpose flour and 1½ tsp. baking powder in a small bowl to combine. Add to pumpkin mixture and fold in with a rubber spatula until just incorporated and no large dry streaks of flour remain (don’t overmix; batter will be lumpy).Step 4Lightly coat the inside of a #12 cookie scoop or ⅓-cup measuring cup with vegetable oil or nonstick vegetable oil spray and evenly divide batter among muffin cups (they will be full). Transfer filling to a piping bag (or a resealable plastic bag with 1 corner snipped off). Working one at a time and dividing evenly, insert bag about halfway into batter and pipe in some filling, ending with a swirl on top of batter. Top each muffin with some streusel, gently pressing to adhere (use all of it).Step 5Bake muffins until streusel is crisp and muffins spring back when gently pressed, 24–27 minutes. Let muffins cool in pan 5 minutes, then turn out onto a wire rack and let cool until just warm or completely.Do Ahead: Muffins can be made 2 days ahead. Store airtight at room temperature.Recipe notesBack to topTriangle