"The hills are smiling," Ms Banerjee, who is in Delhi, tweeted, reserving "special thanks" for voters in Mirik for choosing the Trinamool, the first non-Gorkha party to have an electoral win in the hills in 30 years. Mirik was declared a separate civic body in March.
Darjeeling, Kurseong and Kalimpong, the three other municipal bodies in the hills, were retained by the GJM, but not before a fright in early rounds of counting when the Trinamool led in most municipalities.
In the plains, the Trinamool won all three, Raiganj, Domkal and Pujali. It snatched Raiganj from the Congress and made inroads into another of the rival party's strongholds with its win in Domkal which is in Murshidabad district, dominated by state Congress chief Adhir Ranjan Chowdhury for years.
The Calcutta High Court this morning dismissed the Congress' petition for fresh elections in the three municipalities after opposition parties withdrew candidates from many wards on Sunday, polling day, because of violence and booth capturing, which they blame on the ruling party.
To make matters worse for them, one Congress and two CPM winners of wards in Domkol promptly joined the Trinamool. "This is all Mamata Banerjee's 'karishma (miracle)" exulted Samik Hossain, a leader from her party in Domkal.
Manoj Chakraborty, Congress legislator from Domkal called it "a disgrace." The opposition parties allege today's results would have been different in the plains had they been held with central forces in charge.
"Trinamool did targeted terror," a local BJP leader said.
In the hills, the BJP will be relieved its ally has retained three civic bodies, but the Trinamool's toe-hold through Mirik will be a worry for the party as it embarks on a "Mission Bengal" that envisages installing a BJP government by the next assembly elections in a state where it has had minimal presence till recently.
More immediately, BJP chief Amit Shah has instructed state leaders to ensure that the party wins the maximum seats from Bengal in the 2019 general election.
After the party came second to Mamata Banerjee's party earlier this year in a by-election in West Bengal's Kanthi Dakshin assembly seat - increasing its vote share substantially in the one year since the assembly elections - Mr Shah had thanked voters for making the BJP "the principal opposition party" in the state.
The BJP had won two Lok Sabha seats from Bengal in 2014, increasing its vote share from four to 17 per cent. The Trinamool had won 34 of the state's 42 parliament seats. Last year, Ms Banerjee's party swept the assembly elections for a second term for her as Chief Minister. The BJP won four seats, the party's best performance ever in the state.