Labour has remained the largest party in the chamber but there have been notable gains for the opposition in the local elections.
The red rosette took 20 of the 25 ward seats being contested but that meant there were boosts both for the Conservatives and for independent politicians.
There are now several wards with no Labour councillors as the Conservatives made it a clean sweep of the Orrell ward by getting Living Faith Church minister Steven Evans elected and the Bryn Independents got three out of three seats thanks to stalwart community activist Sylvia Wilkinson.
It was also a good night for the Independent Network (IN) as Jim Ellis returned to the council chamber in Hindley and James Paul Watson secured a thumping victory in Atherton, beating his nearest challenger for Labour by more than 1,000 votes.
Elsewhere, though, Labour managed to get Standish off the independents as veteran opposition representative George Fairhurst lost his seat, coming in third as Debbie Parkinson made it to the chamber at the fifth time of asking.
There were also a couple of very close races, with cabinet member Jenny Bullen scraping back to the chamber by just 35 votes against the Independent Network's Michael Moulding in Ashton and Paul Collins beating independent Gareth Fairhurst by under 100 votes in Shevington with Lower Ground.
John Vickers also had to fend off a strong challenge from IN to beat Deborah Lloyd in Hindley Green, while unaligned independent Clifford Oakley performed strongly in Worsley Mesnes, coming second to former mayor Billy Rotherham with more than 700 votes.
The night's results meant Labour lost three seats overall, while the Conservatives gained one and independents gained two.
That, however, still leaves the red rosette with 57 seats compared to the Tories' eight and the 10 held by independents.
The Conservatives did, though, get the biggest individual vote of the night as more than 2,000 residents turned out in Lowton East to give Kath Houlton another four years as an elected representative.
Afterwards Labour was in philosophical mood after being braced for losses due to these seats last being contested in a general election year while leader of the opposition Coun Michael Winstanley declared himself "very satisfied" with the Conservative outcome.
Turnout was 25.9 per cent in Wigan and 26.8 per cent in Makerfield, confounding predictions earlier in the night that disenchanted voters would stay away from the ballot box in droves.
Abram - David Bowker (Ind) 633, Beverley Bridgewater (Cons) 334, Eunice Smethurst (Lab) 1,117, Frank Swift (Ukip) 387
Ashton - Jenny Bullen (Lab) 1,038, Geoffrey Matthews (Lib Dem) 101, Michael Moulding (Ind Net) 1,003, Mark Temperton (Ukip) 306, Marie Winstanley (Cons) 212
Aspull New Springs Whelley - Andrew Holland (Lib Dem) 489, Chris Ready (Lab) 1,578, Nathan Sweeney (Cons) 526
Astley Mosley Common - Allan Hogg (Ukip) 637, Christine Roberts (Lab) 1,205, Richard Short (Cons) 715
Atherleigh - Mark Aldred (Lab) 821 , Susan Davies (LATT) 135, Paul Fairhurst (Cons) 211, Mary Lavelle (Ukip) 354 , Kevin Lee (Ind Net) 547
Atherton - Marjorie Clayton (Cons) 171, Glenn Marsh (Ukip) 311, Quinton Smith (LATT) 311, David Keir Stitt (Lab) 708, James Paul Watson (Ind Net) 1,826
Bryn - Danny Fletcher (Lab) 1,072, Philip Hayden (Ukip) 284, Denise Melling (Lib Dem) 84, Sylvia Wilkinson (Ind) 1,147, Margaret Winstanley (Cons) 131
Douglas - Margaret Atherton (Cons) 125, John Blondel (Ind) 384, Dalila Garcia Fearn (Ukip) 417, Peter Jacobs (Green) 165, Sheila Ramsdale (Lab) 994
Golborne Lowton West - Stuart Blakeley (Ukip) 420, Gerard Houlton (Cons) 211, Gena Merrett (Lab) 1,011, Susan Spibey (Ind) 568
Hindley - Jim Churton (Lab) 854, Jim Ellis (Ind Net) 1,273, Neil Hancox (Green) 174, Claire Houlton (Cons) 135, John Skipworth (Lib Dem) 70
Hindley Green - Susan Atherton (Cons) 156, Gillian Gibson (Ukip) 370, Joshua Hindle (Lib Dem) 79, Deborah Lloyd (Ind Net) 770, John Vickers (Lab) 905
Ince - Grace Aspey (Cons) 123, Nathan McIntyre (Ukip) 450, Jimmy O’Neill (Ind) 370, Janice Sharratt (Lab) 992
Leigh East - John Dowsett (Lib Dem) 184, Richard Houlton (Cons) 298, James Morley (LATT) 296, Aiden Slack (Ukip) 392, Anita Thorpe (Lab) 995
Leigh South - John O’Brien (Lab) 1,376, Leon Peters (Ukip) 729, Connor Short (Cons) 844
Leigh West - Dane Anderton (Lab) 1,049, Brian Aspinall (Ukip) 613, Jayson Lomax-Hargreaves (LATT) 412, Natalie Smalley (Lib Dem) 161, Denise Young (Cons) 196
Lowton East - Mary Houghton (Ukip) 377, Kathleen Houlton (Cons) 2,111, Garry Lloyd (Lab) 986
Orrell - Denise Capstick (Lib Dem) 318, Steven Evans (Cons) 1,096, Donald McQueen (Green) 314, Stephen Murphy (Lab) 1,043
Pemberton - Craig Buckley (Ukip) 577, David Burley (Lib Dem) 154, Jean Peet (Cons) 202, Eileen Rigby (Lab) 1,127
Shevington with L. Ground - Paul Collins (Lab) 988, Gareth Fairhurst (Ind) 895, Michael Owens (Cons) 356, Joseph Rylance (Green) 336, Derek Wilkes (Ukip) 324
Standish with Langtree - Judith Atherton (Cons) 946, Carl Davies (Ukip) 354, George Fairhurst (Ind) 774, Debbie Parkinson (Lab) 1,038, Neil Stevenson (Lib Dem) 174
Tyldesley - Kerry Ford (Ukip) 473, Stephen Hellier (Lab) 1,037, Julian Marsh (Ind) 887, David Stirzaker (Cons) 334
Wigan Central - Lewis Evans (Cons) 672, Michael McLoughlin (Lab) 1,222, Tony Spencer (Ind) 546, Stuart Thomas (Lib Dem) 268
Wigan West - Steve Dawber (Lab) 1,234, Yamini Gupta (Cons) 181, Will Patterson (Green) 233, Nathan Ryding (Ukip) 544, Caroline Waddicor (Lib Dem) 143
Winstanley - Allan Atherton (Cons) 333, Steven Heyes (Green) 319, Marie Morgan (Lab) 1,017, Scott Sheedy (Ukip) 497, Robert Stevenson (Lib Dem) 242
Worsley Mesnes - Mikah Evans (Cons) 163, Maureen McCoy (Ukip) 383, Clifford Oakley (Ind) 713, Billy Rotherham (Lab) 1,076
Key: Lab - Labour; Cons - Conservatives; Lib Dem - Liberal Democrats; Green - Green; Ukip - UK Independence Party; Ind - Independent; Ind Net - Independent Network; LATT - Leigh, Atherton and Tyldesley Together.