The recruitment marks a new tactic for al-Shabab, underscoring fears voiced by Kenyan intelligence services and MPs.
In one town alone, the BBC has learnt of 26 young men whose disappearance was reported to police because they were suspected to have joined the militants.
Al-Shabab attacked a Kenyan university two weeks ago, killing 148 people.
The attack at Garissa was the deadliest yet on Kenyan soil by the militants. One of the gunmen was a Kenyan national.
Al-Shabab's recruitment of fighters in Kenya's own backyard marks a change of tactic for al-Qaeda's affiliate in East Africa.
The BBC has learnt of scores cases of missing young men in the north-eastern town of Isiolo, who later admitted in phone calls to their parents that they had joined the Islamist group.
Only half of those cases have been reported to the police because of fears of reprisals. There are similar concerns in other parts of the country.
The families of two youths I interviewed who had signed up with al-Shabab were far from being disenchanted school drop-outs.
Instead, they spoke of their sons being among the brightest in their class, high achievers. with professional ambitions.
One, a 17-year-old called Abdulahi, had become fascinated with the teachings of Aboud Rogo, the Islamist cleric who was killed in a drive-by shooting in Mombasa nearly two years ago.
He was on an international wanted list for his involvement in allegedly seeking out new al-Shabab recruits.
The killing of Rogo, which some Muslims blame on the Kenyan security forces, threw Kenya into chaos as Muslim youths took to the street to demonstrate.
A sense of marginalisation, frustration and claims of extrajudicial killings are among the reasons given for why al-Shabab may be finding traction in parts of the Muslim community.
The stubborn problem of youth unemployment is also a factor.
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As part of the Kenyan government's efforts to enlist the help of the Muslim community to fight the radicalisation of Kenyan youth, an amnesty has been offered to young Kenyan men who have been lured into joining al-Shabab.
But one of the most powerful Muslim leaders in the country, Sheikh Abdullahi Salat, warned that widespread mistrust of the security services in Kenya threatens to frustrate investigations.
He claimed that corruption within the police, military and intelligence services was likely to hamper attempts to hunt down al-Shabab.
The Kenyan government, whose anti-insurgency campaign has focused largely on military efforts across the border in Somalia, have described the allegations as a "diversion".
Somalia's Islamist al-Shabab militants are recruiting heavily in north-eastern Kenya, according to evidence gathered by the BBC.