The Blues headed to Lincoln off the back of seven matches undefeated and four straight wins since the Ipswich debacle.
If those demons have not been exorcised, his bold decision to resurrect the three-man central defence at Sincil Bank certainly laid to rest other ghosts.
It’s last outing was that 4-0 humiliation at Fratton Park, the system subsequently torn up and discarded in the desperate search for a winning formula.
Yet, with needs must in the absence of Lee Brown and a suitable left-back replacement, Cowley restored the formation against Lincoln.
The outcome was a 3-0 triumph through goals from Marcus Harness, George Hirst and Reeco Hackett to maintain Pompey’s surge up League One.
Victory was thoroughly deserved too, in a performance brimming with eye-catching displays, particularly from Marlon Romeo, Joe Morrell and Shaun Williams.
Indeed, the brilliant Romeo was denied his maiden Blues goal when he struck the inside of the post in the second half.
As a team, though, Cowley’s men clicked impressively utilising a 3-4-3 system, playing fluently, demonstrating attacking flair and, crucially, resolute at the back.
It is understandable that some members of the Fratton faithful felt some trepidation after learning of Cowley’s tactical switch.
Those fears proved unfounded, however, to highlight Pompey are these days a very different team, irrespective of the formation.
Certainly a happy return to Lincoln for Cowley, who, in three years at Sincil Bank, achieved two promotions and an EFL Trophy win at Wembley.
And, in the here and present, his Pompey side found themselves unbeaten in eight matches and in ninth position – three points off the play-off positions.
Pressed into changing his team through Brown’s absence, Kieron Freeman was recalled to join Sean Raggett and Connor Ogilvie in a back three.
It represented Freeman’s first League One start since Ipswich, while the wing-back roles were filled by Mahlon Romeo and Reeco Hackett.
The former Sheffield United man represented one of three changes to the side which defeated Wimbledon 2-1 through Marcus Harness’ late goal.
Joe Morrell came in for Louis Thompson, while Jacobs was replaced by Hackett, with both omitted players dropping to the bench.
There was also a surprise appearance among the substitutes for Liam Vincent, who has yet to make his Blues bow following his summer arrival.
The left-back has been troubled by injury since the opening few days of pre-season training and, as consequence, is still to feature in a match at any level for Pompey.
Meanwhile, former Imps favourite Sean Raggett was named as captain against his former club in Brown’s absence.
And John Marquis once again missed out through the tendon problem which has sidelined him for the Blues’ last three league games.
Lining up in a 3-4-3, the Blues were presented with a testing time in the game’s early stages, with the hosts enjoying decent possession.
On seven minutes, Ted Bishop tried his luck from just inside the Blues’ box, yet it was straight at Gavin Bazunu, who caught the ball without problems.
At the other end, Hackett’s cross from the left was collected by Ronan Curtis, with back to goal, and the Irishman managed to get off a shot which deflected for a corner.
From that flag kick, the ball eventually fell to Connor Ogilvie on the far side and his powerful angled shot was beaten out by keeper Josh Griffiths.
On 17 minutes, lovely play from Joe Morrell saw him initiate an attack, feeding Marcus Harness, whose ball down the line freed George Hirst on the right.
The striker crossed to Curtis inside the box and he took a touch before dragging a right-footed shot wide of the far post in a decent position.
The hosts’ Freddie Draper found himself clean through on goal on 25 minutes, yet Freeman came across to provide crucial cover and dispossessed the striker before he could shoot.
Raggett became the first player to be booked when, on 29 minutes, he tangled with Draper inside the Lincoln half as they attempted to counter.
He was soon followed by fellow ex-Lincoln player Morrell, again involving preventing a swift counter through the centre of the pitch.
Pompey had by now grown into the game and were looking the better side, enjoying some positive moments, yet the scoreline remained goalless.
Lincoln fans thought they had strong appeals for a penalty on 38 minutes when Hackett raced back to apply a shoulder challenge to the dangerous Lasse Sorensen inside the box.
The Dane crumpled to the floor, but referee Ross Joyce saw no reason to award a spot kick and waved for play to continue.
With half-time approaching, Harness crashed a fierce left-footed attempt from 25-yards, which thudded into the chest of keeper Griffiths as he caught it.
On the stroke of the interval, Hirst embarked on a strong run from his own half which he maintained until he entered the opposition's penalty area.
However, Griffiths beat out his subsequent angled shot to earn the visitors a corner down the right.
During two minutes of time added on the deadlock was broken by the in-form Harness.
Romeo initiated the moment, sliding the ball into the box which eventually fell into the path of Harness, who lashed a first-time right-footed shot into the far corner to make it 1-0.
With no substitutions at the break for either side, Pompey almost extended their lead on 51 minutes.
Curtis cut across from the left and squared the ball for Romeo, who struck a sweet right-footed angled shot from outside the box which struck the inside of the far post and bounced wide.
Hirst won a foul on the hour mark, earning Lewis Montsma a booking, and the resulting free-kick was headed wide by Curtis when perhaps he should have diverted it back across goal.
It was 2-0 to the Blues on 66 minutes with Hirst collecting his first Football League goal.
Harness pushed the ball down the right channel of the box for Curtis, who drilled a delivery across goal and it was diverted home by the on-loan Leicester striker.
The scoreline was completed in the 89th minute when Curtis’ free-kick struck the Lincoln wall and Hackett followed up to stroke the ball home and make it 3-0.
A thumping win for the Blues – and a triumph for the returning three-man central defence.
A message from the Editor, Mark Waldron
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