Caution: when working with chili peppers, be sure to wear disposable food gloves since the oils from the chili peppers is very difficult to get off of your hands and will burn your eyes and other sensitive body parts.
Source Your Jalapeno Peppers
Choose ripe jalapeno peppers that are firm, fresh, and red and wash and dry them thoroughly. You will get about 1 pound of chipotles for every 10 pounds of jalapeno peppers you use. There is an orchard / crop farming operation close to me that grows some incredible varieties of peppers throughout the season. At the end of the season the jalapeno’s turn ripe and they have a surplus – so they sell them by the quarter bushel at a discount.
Prepare the Jalapeno Peppers
You can leave the jalapeno peppers whole, or if you’d like to reduce the drying time you can cut off the stems and / or slice the jalapeno peppers open, being careful not to lose too many of the seeds. If you’d like to take away some of their heat, you can remove the seeds and membranes since that’s where a lot of the jalapeno heat comes from.
I usually take a small paring knife and with a quick circular motion remove the stem and open the end of the pepper allowing air and smoke to penetrate.
Smoke the Jalapeno Peppers
Put the jalapano peppers in a smoker and cold smoke them for 8 to 16 hours. If you don’t have a smoker, there are many good kinds available. Or, if you want to make your own smoker, you can find directions here or here.
Make sure your smoker is very clean before you start smoking the jalapeno peppers, otherwise it may impart stale food flavors into your chipotles. You want the peppers to end up black, dry, leathery, and brittle to make sure the flavor will be preserved. Since this can take a long time, many people will finish off the peppers in a food dehydrator or oven (below 200 degrees) overnight.
Use or Store Your Chipotles
Store the peppers in a cool, dark, and dry place for up to 6 months. You can also make chili powder by grinding up the dried peppers.