Hundreds of Somali and African Union Mission to Somalia (AMISOM) soldiers entered the town on Afgoye, home to the world's largest population of internally displaced people. Before Friday, 400,000 refugees lived on land controlled by al-Shabab, who are notorious for blocking foreign food and humanitarian aid shipments. Many of the refugees had fled to Afgoye from violence, famine and drought in other parts of the country.
Afgoye is considered al Shabab's most important stronghold after the southern city of Kismayo.
The latest push against the rebels comes 10 months after AU forces expelled al Shabab from Mogadishu. Since then, an AU force of Ugandan soldiers has kept the insurgents out of the capital, while a separate offensive from Kenya and Ethiopia have challenged al Shabab in the southeast.
Al Shabab has not made a public statement since AMISOM began its assault on Afgoye on Tuesday, which is uncharacteristic. Militants are believed to have scattered out from the town, and could be hiding in the nearby bushland or villages, although AU troops have captured much of the surrounding area.
They might never recover from this, the spokesman for the AU in Somalia, Lt-Col Paddy Ankunda told the BBC.
The value of expelling al-Shabab from Afgoye, and eventually Somalia, is greater than just protecting refugees. In August, the mandate of the county's transitional government will end and a new government will attempt to establish law and order, something which Somalia hasn't had since the fall of the Siad Barre regime 21 years ago. According to BBC Somali Service editor Yusuf Garaad, if AU forces are able to fully secure the area around the Afgoye Corridor, they could cut al Shabab's territory in half.