Warren Bradley said the Lib Dems would take Liverpool "to the next level"
Confusion abounded in Liverpool after the Lib Dems officially lost control of the council, before claiming they had regained their 10-year hold.
The party lost three seats to Labour and the returning officer recorded a council with no overall control.
But after the result, the party signed up an independent Labour councillor to clinch an unofficial victory.
This means the party have eventually restored their overall majority after first gaining power in 1998.
Council leader Warren Bradley said the signing up of Nadia Stewart had retained "political stability" in the city.
"We have got 46 seats. We are in control in the city," he said.
"It was a tough election for the Liberal Democrats after 10 years of power."
Remaining positive, he told the BBC his party had taken the "popular vote".
He said: "I think we are disappointed but you have got to think the popular votes the Lib Dems have gained in Liverpool, and you've got to think about what we've achieved in the last 10 years.
"We have worked with all our partners to make sure that Liverpool is a place where people want to invest, want to live, want to work and play.
"And it's important to remember that the vast majority of people in this city still want to Liberal Democrats to control it."
But Joe Anderson, Labour leader in Liverpool, described the result as a "disaster" for the Lib Dems.
He said: "We have done remarkably well. We have gained four seats tonight.
"It's a disaster for them. The Liberal Democrats' flagship is well and truly holed. I'm very pleased."
Elsewhere on Merseyside, Labour councillor James Caunce, 89, held onto his seat in Haydock Ward in St Helens, where the Lib Dems have gained in the past two years.
Wirral Council remained in no overall control, as did Sefton.
Labour maintained their control of Knowsley and Halton Borough Council.