President Enrique Pena Nieto's government had balked at extraditing Guzman prior to his prison break in July but the administration has apparently changed tack after recapturing him on Friday.
The attorney general's office said yesterday it received two US extradition requests last year on a slew of charges, including drug trafficking and murder, and that it later obtained arrest warrants to ship him across the border.
"With Guzman Loera's recapture, the respective extradition proceedings will have to start," the office said in a statement, though it did not indicate when the hearings would start.
Once a judge rules on the extradition, the decision is sent to the foreign ministry, which will have 20 days to validate it. Guzman would have another chance after that to legally challenge the extradition.
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One of Guzman's attorneys, Juan Pablo Badillo, vowed to take the case up to the Supreme Court if necessary.
"A legal battle has begun in the constitutional framework that will be very serious, very tough," Badillo told reporters outside the Altiplano prison near Mexico City, where Guzman was sent following his arrest on Friday.
US President Barack Obama's administration congratulated Mexico following the arrest but did not publicly indicate whether it would press Pena Nieto to extradite Guzman.
US politicians called for his immediate extradition as he faces charges in a half-dozen states.
Some questioned Mexico's ability to hold on to Guzman, who previously escaped from another maximum-security prison in 2001 by hiding in a laundry cart with inside help.
"Given that 'El Chapo' has already escaped from Mexican prison twice, this third opportunity to bring him to justice cannot be squandered," said US senator and Republican presidential hopeful Marco Rubio.