The location on North Main, which closed down in 2018, will instead hold administrative offices and other services, according to officials.
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The Salvation Army released a statement admitting the shelter became a burden to the northside community.
SEE RELATED STORY: Some community members call northside Salvation Army closing 'victory for public safety'
Andre Jackson, the man convicted of stabbing Josue more than 20 times on his way home from school, was seen on surveillance video walking into the shelter after the attack.
Neighbors said they wanted more security and other conditions met before the shelter could reopen.
WATCH: Andre Jackson screams "Oh, God!" as he's convicted
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Andre Jackson shouts as jury convicts him of Josue Flores' murder
SEE RELATED STORY: Andre Jackson faces 5 years to life in prison after conviction in 11-year-old Josue Flores' murder
SEE ALSO: Search for justice: Timeline of Josue Flores murder case
How Josue Flores' brutal murder case has unfolded: TIMELINE