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A 45-year-old Kenyan man resident in Canada is facing  charges arising from the deadly poisoning of three-year-old Bernice Nantanda Wamala and the sickening of her best friend during a sleep-over in Scarborough a few months ago.

A Toronto source for the Sun newspaper said Francis Ngugi is the ex-boyfriend of the surviving toddler’s mom and the couple broke up the month before the girls were poisoned but remained friends.

Toronto police alleged a man “accessed a controlled substance” from his work and put it into a package of Golden Morn cereal, which the toddlers ate for breakfast on the morning of March 7 after their sleepover.

“Both children required hospitalisation,” Det. Matthew Wighton, of 41 Division, said in a statement released by police

“One of the children, due to the consumption of the cereal, died in hospital,” he added. “The other child recovered after a lengthy hospital stay.”

An investigation by police and the Ontario Coroner’s Office culminated in an arrest on Sunday.

Ngugi is charged with two counts each of administering a noxious substance to endanger life and unlawfully causing bodily harm, and one count of criminal negligence causing death.

A source told the Sun the “controlled substance” was nitrite, which is used as a preservative in cured meats and other foods.

Over exposure to nitrites can lead to a condition called methemoglobinemia in which the body is deprived of oxygen.

Police have not commented on a possible motive for the alleged poisoning.

Bernice lived with her mom in a highrise on Birchmount Rd., south of St Clair Ave. E., and had a sleep-over on March 6 at her best friend’s apartment in the same building.

“She was healthy, happy, and dancing on Saturday, then the next day she’s gone,” heartbroken mom Maurine Mirembe told the Sun days after her daughter’s death.

Mirembe said the mother of the other girl, also aged three, called her the morning after the sleep-over around 10 am and told her that Bernice was lethargic, vomiting and had soiled herself.

“I knew right away something was really wrong,” she said at the time.

Soon after, Bernice began having seizures, then her fingers, toes, and lips turned grey — a symptom of methemoglobinemia.

After calling 911 and waiting for an ambulance that never showed, a friend drove Mirembe and her daughter to Michael Garron Hospital.

By about 1:15 pm, the little girl was dead.

Bernice’s best friend, meanwhile, also become ill and was taken to Sick Kids hospital where she recovered.

Investigators immediately focused on what the girls ate for breakfast — Golden Morn — an African cereal made of corn and soya.

With help from the Canadian Food Inspection Agency, samples were analysed and soon ruled out any widespread concerns with the cereal product.

After months of testing, police concluded the cereal the girls ate was deliberately contaminated. Ngugi remained in custody Monday awaiting a bail hearing. —Agencies