Authorities accused his Taliban group, also known as Boko-Haram (hausa for Western education is sin), of "engaging in some suspicious activities with security implications," without giving details.
They were, however, granted bail by an Abuja High Court on January 20.
A police officer jubilating over his execution remarked in Maiduguri: "It's good riddance because our judiciary system has many loopholes and there is slim possibility of him being let off the hook."
A theology undergraduate university dropout from the Islamic University of Medina in Saudi Arabia, Yusuf was born on January 29, 1970 in Girigiri village in northeastern Yobe, a state bordering Niger, Chad and Cameroon.
His self-styled Taliban emerged in 2002 in Maiduguri before setting up a camp on the border with Niger, from where they launched a series of attacks on the police.
But officials say they have been in existence since 1995.
"They (militants) have been in existence as far back as 1995, under different names ... but with the same doctrine of intolerance," said Ogan.
His group, opposed to Western education and civilisation, this week was engaged in bloody clashes with security forces in the states of Bauchi, Kano, Yobe and Borno, in which more than 600 people were killed.
The leadership had previously said it intended to lead an armed insurrection and rid society of "immorality" and "infidelity".
Yusuf was married to four wives and father of 12 children.
His bullet-riddled body was displayed at a police headquarters with one hand in a sling, suggesting he was wounded in fighting before his capture Thursday.
------------------------------------------------------------------------------------------------------------------------------