Umaish Ramrattan, 61, of Ajax, Ont., was arrested after a raid at a warehouse in Brampton on Wednesday, police said.
Police seized 26 skids of property they believe had been donated to the Salvation Army including toys, school supplies, cleaning products and food.
Ramrattan faces 40 charges and is scheduled to appear in court on Jan. 4.
The alleged thefts took place at the Salvation Army's warehouse facility on Railside Road.
The facility's former executive director, David Rennie, was charged earlier this week with theft, possession of property obtained by crime and criminal breach of trust.
Rennie, who was in charge of the warehouse where the missing toys were sorted and stored, was fired a week ago.
The Salvation Army released a statement Thursday that praised police and said Ramrattan had no connection with the charity organization.
"As we have stated publicly in the past, we have not had a business or personal relationship of any kind with the second individual arrested or his company," the statement said.
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