Whisk together flours and salt in a medium bowl. Set aside 2 tablespoons of cheese. Stir in olive oil, water, remaining cheese, and jalapeño. Mix until just combined, careful not to overwork the dough. If needed, add another tablespoon of water to moisten.
Line a large baking sheet with parchment paper. I used a rimmed sheet, but an unrimmed sheet would work too. Transfer cracker dough to baking sheet and roll out it out as thin as you can—about the thickness of a saltine. Use a knife or pizza cutter to mark dough into rectangles. (Don't cut the dough all the way through, just draw lines on it.) Sprinkle tops of crackers with reserved cheese and sea salt.
Bake for 20–30 minutes or until crisp and just beginning to brown. Baking time depends on the thickness of the crackers, so be sure to keep an eye on them! Allow to cool completely, then break along lines. Store crackers in an airtight container; if they get stale, bake at 225°F for 10 minutes or until crisp.
Notes
For spicier crackers, add a second jalapeño or use a hotter pepper.
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