However, they lost a seat to the Liberal Democrats who saw their second councillor, Martin Christopher, voted into Abbey Ward.
A total of 18,285 people voted – a turnout of 29.07%.
The final result saw Labour win seven of the 11 seats available with the Conservatives taking three and the Liberal Democrats one.
The results leaves the political make-up of the council at 22 Labour and nine Conservative, and two Lib Dems.
It was previously 22 Labour, 10 Conservative and one Liberal Democrat.
In North East Lincolnshire, the Conservatives secured a comfortable victory.
Seats on all 15 wards were up for grabs with the Conservatives going into the election holding 32 of 42, and 10 being contested.
The council now has 30 Tory councillors, eight for Labour, three for the Lid Dems and one independent.
Lincolnshire residents will next go to the polls in the Sleaford by-election on Thursday, May 26.
The by-election comes after Conservative Michael Kent resigned as North Kesteven District councillor for the Sleaford Quarrington and Mareham ward.
Labour, Conservative and Lincolnshire Independents will all be competing for the seat.
The candidates have been announced as:
Paul Andrew Edwards-Shea (Labour Party)
Bob Oldershaw (Lincolnshire Independents – Sleaford)
Mark Anthony Smith (Conservative Party)
Polls will be open between 7am and 10pm.