BBC Radio Manchester will also bring listeners highlights from Band on the Wall as part of a special programme from 26 March at 20:00.
The Radio Manchester Breakfast Show with Joe McGrath will continue to follow the festival from Friday 27 March at 06:00.
Samantha Moy, head of 6 Music, said: “Independent grassroots venues are vital to the UK’s music ecosystem and at 6 Music, we’re proud to support what they do.
“So, it makes sense for the next evolution of the 6 Music Festival to take place in these special spaces, collaborating with new partners and celebrating Manchester’s incredible music legacy, as well as the next generation of artists.”
Mayor Andy Burnham added: “Greater Manchester’s music scene has always been driven by its grassroots venues and independent spirit.
“They’re vital to nurturing new talent and keeping our cultural life vibrant.”