The first bite is all contrasts — a shatteringly crispy everything bagel crust giving way to a thick, tangy cream cheese filling that practically melts into the tender zucchini shell beneath it. These air fryer zucchini boats take the beloved deli pairing of cream cheese and everything bagel seasoning and turn it into a proper keto dinner, stuffed with two kinds of cheese and blistered golden in about fifteen minutes flat. Sharp cheddar melts across the top in bubbly, stretchy ribbons while the sesame-studded crunch stays perfectly toasty underneath. Think of it as a loaded bagel without the bagel — and somehow better for it.

Each two-boat serving delivers 48 grams of fat and 21 grams of protein against only 8 grams of net carbs, placing this squarely in ideal keto territory with roughly 77 percent of calories coming from fat. The cream cheese and cheddar do the heavy lifting on both fat and protein, while the naturally low-carb zucchini shells keep the total remarkably restrained for such a generous, cheese-stuffed portion.

These boats come together fast enough for a Tuesday night but look impressive enough for company. The filling can be mixed a full day ahead, and the everything bagel crunch topping takes about two minutes to stir together. Pair them with a simple butter lettuce salad or some garlic-wilted spinach for a complete meal that moves from cutting board to table in under half an hour.

Ingredients (serves 4)

For the cream cheese filling:

  • 8 oz (225g) full-fat cream cheese, softened at room temperature for 20 minutes
  • 1 cup (113g) shredded sharp cheddar cheese
  • 2 large eggs, lightly beaten
  • 2 green onions, thinly sliced (white and green parts separated)
  • 2 cloves garlic, minced
  • 1/2 tsp smoked paprika
  • 1/4 tsp freshly ground black pepper
  • Pinch of kosher salt

For the zucchini boats:

  • 4 medium zucchini, about 7–8 inches (18–20cm) long
  • 1 tbsp (15ml) avocado oil
  • 1/2 tsp kosher salt

For the everything bagel crunch:

  • 2 tbsp (14g) almond flour
  • 2 tbsp (18g) everything bagel seasoning
  • 1 tbsp (14g) unsalted butter, melted
  • 2 tbsp (10g) finely grated Parmesan

For topping and garnish:

  • 1/2 cup (57g) shredded sharp cheddar cheese
  • Fresh chives, snipped, for garnish
  • Flaky sea salt (optional)

Instructions

  1. Prep the zucchini. Cut each zucchini in half lengthwise. Use a small spoon or melon baller to scoop out the seeds and soft center, leaving a sturdy shell about 1/4 inch (6mm) thick. Blot the insides firmly with a folded paper towel, then set the halves cut-side down on a clean towel for five minutes while you make the filling. This step is critical — the drier the zucchini goes into the air fryer, the crispier and sturdier the boats will be. Brush the cut sides lightly with avocado oil and season with the 1/2 teaspoon kosher salt.

  2. Make the cream cheese filling. In a medium bowl, stir the softened cream cheese with a fork or spatula until completely smooth with no lumps remaining. Add the 1 cup shredded cheddar, beaten eggs, white parts of the green onions, garlic, smoked paprika, pepper, and salt. Mix until evenly combined. The texture should be thick and spreadable, not pourable — if it seems loose, the cream cheese was too warm.

  3. Build the everything bagel crunch. In a small bowl, toss the almond flour, everything bagel seasoning, melted butter, and Parmesan together with your fingers until the mixture forms coarse, sandy clumps. Set aside.

  4. Fill the boats. Divide the cream cheese mixture evenly among the 8 zucchini halves, mounding it slightly above the rim. Press it in gently so it fills the scooped channel completely and makes good contact with the walls. Sprinkle the everything bagel crunch over the top of each boat, pressing it lightly into the filling so it sticks.

  5. Air fry. Preheat your air fryer to 375°F (190°C) for 2 minutes. Arrange the boats in a single layer in the basket — you will likely need to cook in 2 batches unless you have a large 6-quart or bigger model. Air fry for 12–14 minutes until the zucchini is fork-tender, the filling is puffed and golden, and a toothpick inserted into the center comes out with just a thin layer of melted cheese clinging to it rather than raw batter.

  6. Add the cheddar cap. Scatter the remaining 1/2 cup cheddar evenly over the hot boats. Air fry for 2 more minutes until the cheese melts into a bubbly, golden blanket with a few lightly browned spots.

  7. Rest and garnish. Transfer the boats to a serving platter and let them sit for 3 minutes — the filling firms up slightly as it cools, making them much easier to pick up and eat. Scatter the reserved green onion greens, snipped chives, and a pinch of flaky sea salt over the top. Serve hot.

Nutrition per Serving

Nutrient Amount
Calories ~550 kcal
Fat ~48g
Protein ~21g
Total Carbs ~10g
Fiber ~2g
Net Carbs ~8g

Nutrition is approximate and calculated from stated ingredient quantities using USDA data for full-fat cream cheese, sharp cheddar, and standard everything bagel seasoning.

Tips & Variations

Choose the right zucchini size. Medium zucchini (7–8 inches long, about the thickness of your wrist) are ideal. Smaller ones hold too little filling to feel like a real dinner. Larger ones have a spongy, seedy core that releases a lot of water and can make the boats collapse. If you can only find large zucchini, scoop out extra flesh aggressively and increase the filling by about a quarter.

Pat the insides dry — really. This is the single most important step for crispy results. Zucchini is roughly 95 percent water by weight. After scooping, press a folded paper towel firmly into each cavity and let the halves sit cut-side down on a towel for a full five minutes. The drier they go into the air fryer, the better they hold their shape and the crunchier the topping stays.

Make the filling ahead. The cream cheese mixture keeps beautifully in a covered bowl in the fridge for up to 24 hours. Pull it out 15 minutes before you plan to stuff the boats so it softens enough to spread evenly. The crunch topping can be mixed ahead too — store it separately in a small jar at room temperature for up to 3 days.

Watch for hidden carbs in the seasoning. Some store-bought everything bagel seasonings contain sugar, maltodextrin, or starch-based anti-caking agents that add sneaky carbs. Read the label before you buy. Trader Joe's, McCormick, and Whole Foods 365 versions are all sugar-free. You can also make your own by combining equal parts white sesame seeds, black sesame seeds, poppy seeds, dried minced garlic, dried minced onion, and flaky salt.

Switch up the cheese. Pepper jack brings gentle heat that plays well against the sesame-onion topping. Gruyere gives a nuttier, more complex melt on top. Fontina works beautifully if you want something milder and extra stretchy. Stick to full-fat, aged, or semi-firm cheeses to keep the fat-to-carb ratio in line — soft fresh cheeses like queso fresco or fresh mozzarella tend to weep moisture and won't form that satisfying bubbly crust.

Frequently Asked Questions

Will these boats work in a conventional oven instead of an air fryer?
Absolutely. Preheat your oven to 400°F (200°C) and arrange the stuffed boats on a parchment-lined rimmed baking sheet. Bake for 20–22 minutes until the filling is puffed and golden and the zucchini is tender. Add the final layer of cheddar and broil on high for 2–3 minutes to get that bubbly, browned cap. Oven-baked boats take a bit longer but have the advantage of cooking all 8 at once without batching. The crunch topping gets slightly less crispy in a conventional oven due to less direct air circulation, but the results are still excellent.
What can I use instead of almond flour in the crunch topping?
Finely ground sunflower seed meal is the closest swap — it gives a similar sandy crunch without any nut allergen concerns. Hemp hearts work well too but produce a softer, chewier texture rather than a true crunch. Coconut flour functions in a pinch, though it absorbs more fat, so increase the melted butter to about 1 1/2 tablespoons if you go that route. Any of these alternatives keep the topping nut-free for allergy households while staying firmly keto.
How do I store and reheat leftovers?
Refrigerate leftover boats in a single layer in an airtight container for up to 3 days. Reheat them in the air fryer at 350°F (175°C) for 5–6 minutes until the cheese is bubbly again and the zucchini is warmed through. The microwave works if you are in a hurry (90 seconds on high), but the crunch topping will soften considerably. Do not freeze these — zucchini releases too much water during thawing, and the filling becomes grainy rather than creamy once defrosted.
Can I make a dairy-free or vegan keto version of these boats?
For dairy-free, swap the cream cheese for a cashew-based alternative like Miyoko's or Kite Hill, and replace the cheddar with a vegan shredded cheese that melts well (Violife is a reliable choice). Use nutritional yeast in place of the Parmesan in the crunch topping and coconut oil instead of butter. Keep the eggs for binding the filling. For a fully vegan version, replace the two eggs with 2 tablespoons of ground flaxseed mixed with 5 tablespoons of warm water — let the mixture gel for 10 minutes before stirring it into the filling. The texture will be slightly softer but still holds together well.
My zucchini boats came out soggy on the bottom — what went wrong?
The most common cause is skipping or rushing the drying step after scooping out the seeds. Zucchini holds an enormous amount of moisture, and steam trapped underneath in the air fryer basket has nowhere to go. Next time, blot the cavities thoroughly and let the halves sit cut-side down on paper towels for a full five minutes before oiling and stuffing. Also make sure the boats rest in a single layer with space between them so hot air circulates freely on all sides. If your air fryer has a solid (non-perforated) basket bottom, consider placing the boats on a small wire rack insert to elevate them slightly and allow steam to escape downward.