Fresh peppers will keep up to one week when stored whole and unwashed in a paper bag in the refrigerator. The peppers can also be frozen up to three months.

Green Jalapeño chile peppers are best suited for both raw and cooked applications such as roasting, baking, grilling, simmering, and stir-frying. The green peppers are considered to be one of the most versatile culinary varieties and can be chopped into salsas, blended into hot sauces and marinades, diced into dips and guacamole, or cooked into jelly. The peppers can also be sliced into stews, soups, and chilis, baked into muffins and bread, chopped for ceviche, sprinkled over pizzas, or used as a topping over nachos and tacos. In addition to cooked applications, Green Jalapeño chili peppers are a common pickling pepper and can be used as a condiment on hot dogs and sandwiches. Their thicker flesh also makes them ideal for stuffing with vinegar, tomatoes, garlic, cilantro, beans, corn, cheese, cream-based sauces, pork, and ground beef. Green Jalapeño chili peppers pair well with fruits such as kiwi, pineapple, mango, and watermelon, cheeses such as feta, cheddar, and cream cheese, meats such as bacon, pork, beef, and poultry, shrimp, tomatoes, cucumbers, broccoli, carrots, radish, corn, avocado, potatoes, cilantro, and arugula.

Green Jalapeño chili peppers are an excellent source of vitamin C and contain copper, magnesium, vitamins A, E, and K, folate, manganese, fiber, potassium, and iron. The peppers also contain capsaicin, which is the chemical compound that triggers the brain to feel heat or spice. Capsaicin has been shown to have anti-inflammatory properties and can help aid in digestion.