How to Smoke Chipotle Peppers {A Step-By-Step Guide

I have a slight obsession with chipotle peppers. I love chipotles for their distinctive smoky flavor and their peppery heat.

Chipotle peppers are common in Mexican dishes, however, the chipotle flavor has become pretty popular here in the states. Chipotle peppers are found in many dishes and can have a mild or spicy flavor depending on how they are used. From enchiladas, soups, sauces, and even ground into a fine powder and added to spice rubs and barbecue sauces.

What exactly are chipotle peppers?

Simply stated, a chipotle pepper is a dry-smoked jalapeño pepper. Chipotle peppers are most commonly made from fully-ripened red jalapeños. The jalapeños are allowed to fully ripen on the jalapeño plant as long as possible before they harvested for smoking.

Chipotle peppers date back to the Aztecs. The Aztecs smoked the chilies to prevent them from rotting. The peppers were smoked because their skins are too thick, making them too difficult to dry before rotting. This same “smoke drying” process is similar to how meats are cured, allowing them to be stored for longer periods of time.

A jalapeño pepper’s natural heat is retained during the smoke-drying process. Add chipotle peppers to any dish that needs a kick of smoky flavor. Jalapeños are typically 5,000 to 10,000 Scoville Units, which is on the bottom end of the scale. The heat is usually quite mild producing great flavor without overheating your mouth. They aren’t what David and I call “stupid hot”, so we enjoy them very much.

With the exception of my jalapeño plant, José (who just turned 4 years old) jalapeño peppers are usually a summer crop in Virginia producing jalapeños into the early fall. At the first threat of frost, I take José inside for the winter. While inside, I pluck off all of the blooms and try my best not to let him produce peppers while inside. I try to keep him as dormant as possible, only watering him about once a week. 

— Does anyone know of another jalapeño plant this old? 

José produces peppers all summer long, and because of his confined growing space, and age he does not produce very large jalapeños, which makes smoking them an ideal way to preserve the harvest and gives us new ways to add flavor to dishes. David and I made our first batch of chipotle peppers from José’s jalapeños. We are so delighted with the results.

Let me share the process with you!

How to Smoke Chipotle Peppers

CAUTION: PEPPERS CONTAIN CAPSAICIN, WHICH MAY CAUSE A CHEMICAL INTERACTION AND IRRITATE YOUR SKIN AND EYES!! Based on painful experience, I highly recommend that you purchase some disposable food handling gloves before starting this smoking adventure.

Step 1: Choosing the jalapeños

Fully ripened jalapeño peppers are best for making chipotles. However, green jalapeños you can use but they will take longer to smoke. It is very important to use firm peppers without soft spots, with good color and tight stems. The fresher the peppers the better the results. Also, it is important to keep the size of the jalapeños consistent so that they will finish smoking at the same time. The larger the pepper, the more smoke it will require to dry out.

Carefully wash the jalapeños, and double-check them for blemishes and soft spots.

You can smoke the jalapeños just as they are with the stems, seeds, and membranes intact but you can reduce the overall drying time, by cutting off the tops, which allows the smoke to get inside and out of the jalapeños, absorbing more smoke flavor.

We chose to cut off the tops so that more smoke flavor could be absorbed leaving the membrane and seeds intact. The membrane and seeds are where the spicy heat of a jalapeño lives. If you want a milder pepper, you can remove them, otherwise leave them intact, but be careful when handling them so you do not lose too many seeds.

Step 2: Choosing the Wood

The most important ingredient to chipotles is the type of wood for smoking them. When smoking chipotles, you want to use a pretty mild wood. You can use fruit woods such as apple, but hickory and oak are fine too. In Mexico, pecan wood is the traditional wood to smoke chipotles. So pecan wood we used to smoke our chipotles. Use whatever wood you like, just make sure you have a good supply for the long smoke.

Step 3: Prepare the Smoker

For this project, we chose to use David’s 18-inch Weber Smokey Mountain Cooker. We felt that since the jalapeños need such a gentle heat that the fire would be far enough away to give the jalapeños the low even smoke they desire.

Make sure you start out with a good clean smoker. Grease and oils leftover from a previous meat smoke can leave a nasty flavor on the chiles, so make sure the grates are clean.

It’s important to keep in mind that you don’t want to cook the chipotles you want to slowly smoke them until dry. It is very important to maintain a low temperature while producing a good smoke. Ultimately, the length of the smoking time will depend on the moisture in the jalapeños. If the jalapeños are large and green, it could take more than 24 hours, so plan on adding coals to the fire periodically.

Prepare for a long smoke and start the fire, using a mixture of charcoal and wet and dry wood chunks or chips.

Step 4: Smoking the Jalapeños

To allow plenty of time for smoking the jalapeños, pick a day when you are planning to be home all day and possibly into the next. Fire up the smoker as early in the morning as you can to get those jalapeños smoking.

When the smoker or grill is the ideal temperature range, you are ready to smoke, place the jalapeños on the rack in a single layer leaving some space between each jalapeño. If you are using smaller chipotles, you may want to use a grilling tray, larger jalapeños should be just fine. After you place the jalapeños on the rack toss a hand full of the soaked wood chunks and some dry wood chunks onto the coals and close the lid.

Keep a close eye on the fire and try to keep the temperature consistent at about 180 degrees F. David likes to use a combination of dry and wet wood chunks, alternating between the two. The dry gives a quick intense smoke and brings the heat up. The wet wood chunks provide a lower, slower smoke and bring the heat down. Heat adjustments are made using this technique in addition to opening and closing the smoker’s vents.

TIP! A smoking thermometer with a probe for the grate like the ThermoWorks Smoke™, that tracks the temperature of the grate with high and low temp alarms takes a lot of the guesswork out of the smoking process and allows you to identify hot and cold zones.

Unless you have hot spots, you don’t have to move jalapeños around or rotate them. In fact, it is best if you move the jalapeños as little as possible. The jalapeños will start to dry and turn black and become leathery when smoked. The chipotles are done smoking when they are completely dry, brittle, very lightweight and have a rich dark color.

We smoked these very small jalapeños for about 14 hours.

Run Out of Time? Don’t worry!

Smoke drying peppers is an art form. Don’t worry if your chipotle peppers don’t turn out the first time. There are many variables when smoking chipotles and sometimes it can take up to 48 hours to completely dry out a batch of jalapeños. Very few people have that amount of time to smoke chipotles for that amount of time. Chipotles will lose their flavor and could possibly spoil if they are not completely dry. At this point, you can refrigerate until needed or freeze them to help preserve them.

If you run out of time before completely drying the jalapeños, you can finish them in the oven. Put the oven on the lowest temperature setting possible directly on the baking rack is best. However, if the chipotles are too small you may have to use a grilling basket. If you don’t have a grilling basket, then use a sheet pan as the last resort. Just keep in mind a pan will hinder the drying process and will take even longer.

A word of caution, finishing the chipotles off inside the oven may make your house smell a little smokey, so don’t say we didn’t warn you.

Storing Chipotle Peppers

It’s important to know that smoked chipotles still have some moisture content even though they have been dried, but smoked chipotles have an indefinite shelf life if stored properly. It’s hard to say how long they will remain fresh. Usually, dried chilies can remain fresh for up to 100 to almost 200 days before they start to lose their flavor, but there is no guarantee.

You can store the dried chipotles inside a mason jar with a lid in a cool, dry place. You can also try plastic bags, but chipotle peppers are very potent and are very smoky. The smoke smell may seep through plastic bags into your cabinet.

Freezing the chipotles is probably the best method for storing your chipotles. Freezing chipotle peppers will slow down decomposition and almost guarantee they keep their freshness. Chipotle peppers must be used immediately after they are defrosted. Due to the moisture content, the chipotle peppers are vulnerable to mold.

It’s also worth mentioning that if you defrost them to make powders you may find that they clump. The clumps do not affect the flavor and can be broken up. It may be best to make powders before freezing to preserve integrity.

Uses For Chipotle Peppers

Use chipotles in anything you want to have a smoky flavor without even having to light the grill. Chipotles come in handy when the weather outside it too bad to light the grill, especially on winter days.

One of the easiest ways to use smoked chipotles is to grind the chipotles up into a fine powder. To make chili powder, all you need is a coffee grinder. I use an expensive coffee grinder that sells on Amazon for around $15.00. It also grinds black peppercorns beautifully!

My personal favorite way to use chipotles is to rehydrate chipotles by placing them in very warm water for thirty minutes to one hour. This makes it easier to cut up and add them to your favorite recipes. Imagine how good chipotles would be in this Classic Barbecue Sauce. YUM!

We hope this step-by-step guide to smoking chipotle peppers allows you to preserve your jalapeño harvest and gives you a great way to add new flavor to your dishes. Chipotle in adobo sauce, chipotle chili salt, and chipotle dips are just a few more recipe ideas.

What will you use chipotles for? Comment below!