Curtis Flournoy, 32, a resident of North Carolina, faces many charges, including ethnic intimidation and burning a commercial building.
He was charged for attacking the store situated in a predominately Indian locality in Charlotte city.
A hearing is scheduled in the first court appearance today for Flournoy, according to Mecklenburg County court officials.
The attack last week had left with a note signed "White America" which threatened to "torture" the refugee business owners if they "did not go back to where they came from", police said.
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After the incident, officers were called to a fire at the Central Market.
On arrival, officers were advised by the Charlotte Fire Department that the fire was contained to the front door and burned itself out by their arrival, they said, adding that one of the windows in the store's door had been broken with a rock and a note signed "White America" left near the door.
The note stated "the suspect did not want any refugee business owners and that they would torture the owner if they did not leave and go back to where they came from," they said.
Dhimel, a Bhutanese refugee who moved to the US from Nepal in 2010 and started his business in 2014, said the letter is a sign that people don't understand the importance of immigrants and refugees in the community.
Investigators say video footage of the incident showed a black male suspect with a short goatee wearing a gray hoodie under a black coat, light jeans and black shoes, police said.
People from India make up Charlotte's second largest concentration of immigrants (just below Hispanics) with 12,300 people, the report said.