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Heat oil in a large vessel over medium-high heat. Add onions and cook until transparent, about 5 minutes. Add tomatoes, red chili powder, and turmeric and reduce heat to medium. Cook until the tomatoes start to lose their shape and the oil begins to separate, about 15 to 20 minutes (optional- you can pick out and discard the tomato skins with tongs once the tomatoes have broken down). Stir periodically to prevent the mixture from burning.
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Add chicken, ginger garlic paste, red pepper flakes, and salt. Sauté until the chicken is cooked through, about 20 to 25 minutes.
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Reduce heat to medium-low and mix in coriander seeds, cumin seeds, ginger, green chili, and cilantro. Cover and simmer the karahi chicken for 10 minutes. Remove from heat and sprinkle in dried fenugreek and black pepper. Cover and allow the flavors to infuse for 10 minutes before serving.