The 38-year-old former actress was wearing a casual khaki Staud dress, with a light headscarf wrapped around her head.
Prince Harry did his part to honour tradition, by taking off his shoes before stepping inside the sacred space.
WATCH: Meghan Markle wears headscarf on South African mosque
Meghan and Harry met with Father Lapsley when they arrived at the mosque, an equal rights campaigner who lost both hands and went blind in one yee following a letter bomb attack.
The Royal couple were seen hugging and chatting with people both outside and in the mosque, with one photo capturing the sweet moment where Meghan leant in to hear a little girl's secret.
Duchess of Sussex visits Auwal Mosque on Heritage Day
Getty
Prince Harry has recently gushed over his wife Meghan Markle during the pair's Royal tour, describing the Duchess of Sussex as 'the best mum'.
The Duke and Duchess of Sussex were visiting Monwabisi Beach, near Cape Town's Khayelitsha township, when talked quickly turned from parenthood to mental health.
The royal couple were visiting the 'Waves for Change' charity, which focuses on helping young people's mental health through surfing.
Prince Harry and Meghan visiting Monwabisi Beach
Getty
In footage captured of the couple, a clearly moved Prince Harry and Meghan Markle spoke about the incredible work of the Waves for Change charity.
"You know what's so amazing about being here today is that you can see there is so much good happening here in the world," Meghan began.
"There's so much positivity and there's all this diversity and inclusivity, I think the focus is on that and that's why it's so great that you're here today."
Milly HaddrickMilly is a journalist who passionately devours all the latest and juiciest news. A devout tea enthusiast who's a firm believer in quality downtime, Milly's weekends are usually spent relaxing with a big plate of food, a nice cuppa and the crossword.