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Step 1
Place chipotle peppers in a bowl and cover the peppers with boiling water. Place a pot lid or plate on the surface to keep the peppers submerged. Leave them soak for 20 minutes. Drain the peppers, reserving 1 cup of the soaking liquid.
Step 2
Combine 4-5 chipotles, 1 cup soaking liquid, tomato puree and honey in a blender or food processor. Process until smooth. Set Aside.
Step 3
Heat olive oil in a saute pan over medium heat. Saute the onions, garlic, salt, pepper and spices until the onions are soft, about 5 minutes. Add the tomato puree and the remaining whole chipotle peppers to the pan.
Step 4
Add the vinegar and cook for another 5-10 minutes until the sauce has the consistency of a thick tomato sauce. If the sauce is too thick add a little more water, if the sauce is too thin cook a little longer.
Step 5
Chipotles in Adobo will keep for several weeks in the refrigerator and the flavors will continue to develop or they can be frozen for long term storage.