Shekau is reported to have begged on the streets of Maiduguri before he eventually joined Boko Haram.
She made this discosure during an interview with Voice of America in her village named Shekau in Yobe State.
According to Falmata, Shekau left his hometown as a young boy to continue his Islamic education in Maiduguri where he eventually met Mohammed Yusuf, the founder of Boko Haram.
The almajiri system was established as an organised system of education for learning Islamic principles, values, and theology with pupils migrating from their homes to other places or to a popular teacher in the quest for Islamic knowledge.
Even though the system was initially funded by the state and pupils were famed for engaging in menial jobs to fund the system, they are now more associated with begging on the streets to make ends meet.
According to the report by VOA, it is believed that Shekau himself begged on the streets of Maiduguri before he fell in with Yusuf's group who was a vocal advocate against western education.
During a military crackdown on the group in 2009, Yusuf and hundreds of other Boko Haram followers were killed, paving the way for Shekau to take control of the group and wage a bloody war against the Nigerian establishment, killing around 30,000 and displacing millions from their homes in an insurgency that has lasted nine years.
Falmata said she has not seen her son since he joined Yusuf and disclosed that she prays to God to touch his heart to put an end to his atrocities.
She said, "I don't now if he's alive or dead. I don't know. It's only God who knows. For 15 years I haven't seen him.
"Since Shekau met with Mohammed Yusuf, I didn't see him again. Yes, he's my son and every mother loves her son, but we have different characters.
"He brought a lot of problem to many people. Where can I meet him to tell him that these things he is doing is very bad? He brought many problems to many people, but I am praying for God to show him the good way."
She also expressed disappointment at how her son has turned out, saying it's not the values she instilled in him.
"He just took his own character and went away. This is not the character I gave him. I don't know what this type of behavior is. It's only God who knows," she said.
The VOA report also revealed that Shekau's father was a local district Imam before he died a few years ago.
Since he took over the reins of Boko Haram after Yusuf's death in 2009, Shekau has been the face of Boko Haram's reign of terror which has led to the death of thousands and displacement of millions.
He has attacked schools, markets, mosques, civilian settlements, military bases and, at some point, took complete control of some local government areas in the country.
His group most notably abducted 276 female students from Government Secondary School in the town of Chibok in Borno State, an act that garnered the group international attention and condemnation.
The Nigerian government has claimed several times that the Boko Haram leader was killed by troops, but he's been known to emerge to discredit those reports every time.