Flames and thick smoke shooting from the roof could be seen for miles throughout the northwest suburbs.
Fire spread rapidly and destroyed the clothing, furniture and other merchandise.
Witnesses at the Harvest Bible Chapel across the street said they saw the fire start as storms rolled through Friday afternoon.
"We were standing by our entrance there and looking across the street and watching lightning bolts flash across the sky, and one we saw come down and hit the back of the WINGS building - hit the transformer, it was like a bottle rocket shot off in the sky, and then several more pops as that just spread from one side to the next," said witness John Smith.
Firefighters responded quickly, but there was nothing they could do to salvage the building. All they could do was contain the damage.
The store served as a fundraiser for homeless and abused women and children, and it was run largely by volunteers. It sold donated items.
"Everyone is just devasted," said Teri Chammer of Women in Need Growing Stronger, or WINGS. "It's part of what we do."
"I donate a lot of stuff there," said neighbor Susan Schwietz. "I shop there, stop in there once or twice a week."
The WINGS organization has been around about 25 years. They provided extended housing for about 400 women and children last year.
This was one of three WINGS facilities in the area, but it was the first built - in 1999.
"We're a strong organization - we're resilient - we're gonna come out of all of this fine," said Chammer. "It is just a mess we're going to have to work through."
The store lost power just before the fire and was actually evacuated, so no one was injured.