The boy's mother, Elizabeth Navarro told CNN that her husband was trying to get clean.
"There was a knock on the door. My husband said 'who's that?' Then I heard two gunshots," Navarro, a pregnant mother-of-5, said.
Both her husband of 11 years and her 6-year-old son died in the attack.
Those killings - of anyone suspected to take or sell drugs - have become common in the Philippines' capital since President Rodrigo Duterte declared his war on drugs almost six months ago.
Since Duterte became President on June 30, almost 6,000 people have been killed in the Philippines. Over half of those killings are estimated by the Filipino police to be extrajudicial or vigilante-style killings, CNN reports.
Additionally, over 40,000 people have been arrested.
On Monday, Duterte admitted to himself killing drug users when he was mayor of Davao:
"In Davao I used to do it personally. Just to show to the guys that if I can do it, why can't you. And I'd go around in Davao with a motorcycle, with a big bike around, and I would just patrol the streets, looking for trouble also. I was really looking for a confrontation so I could kill," Duterte said during a speech at his presidential palace.
Duterte's spokesman has since told the BBC his comments "should not be taken literally" after senators said his comments might be an impeachable offence.
A recent survey showed over 60% of the population were satisfied with the Filipino leaders in the fourth quarter of 2016.