Madonna appeared before Justice Fiona Mwale amid tight security, accompanied by two unidentified children and several other people, before being driven away in an SUV vehicle.
She was spotted as she entered at the court when she entered judges chambers and was later seen carrying a child, believed to be one of the two she wants to adopt.
One of her entourage was said to be carrying another child, according to Nyasa Times, and the singer was driven off in a KIA Sportage SUV.
Madonna's trip to Malawi last year was the first time in nearly two years that she visited the country, where she has at times been embroiled in controversy after her earlier adoptions.
She was stripped of her VIP status by former president Joyce Banda's government in 2013 and accused of being 'uncouth' and wanting eternal gratitude from the impoverished country for adopting the two children.
But Banda was ousted in 2014 elections and the new president, Peter Mutharika, moved to repair relations, saying 'my government has always been grateful for the passion Madonna has for this country'.
Last July, Madonna said she would not revive plans for a $15 million academy for girls in Malawi, which was cancelled amid allegations of mismanagement - leading to her tiff with Banda.
It is now up to the court to decide whether to grant the adoption order, Malawi government spokesman Mlenga Mvula said.
The singer will have to wait a week before hearing the decision on her application.
It is unclear whether she will wait in the country until the decision is made.
Madonna adopted David Banda, now 11, in 2008 and a year later adopted Mercy James, now aged 10.