The charity promotes an end to violence and racism against teenage girls living in poverty.
It was the first time she was seen since she and her husband, Prince Harry, announced their royal family split.
It also comes in the midst of her father, Thomas Markle, saying he will testify against her.
The picture was shared on the centre's Facebook page with the caption, "Look who we had tea with today! The Duchess of Sussex, Meghan Markle".
Markle visited the centre - which provides basic needs and support services, as well as skills development to disadvantaged women - "to discuss issues affecting women in the community".
“Here we come Düsseldorf! The new home for the 2022 and sixth Invictus Games,” Harry captioned the post, which showed a video montage of past games," he said.
Harry set up the event, so those Armed Forces who take part can show the world what they’re capable of in a series of adaptive sports, ranging from wheelchair basketball to indoor rowing.