Just when Arsenal had finally looked to have built some momentum with three wins in a row, they were undone late on by Tottenham Hotspur and then succumbed to a humbling defeat at Rennes.
Emery's men now have it all to do in next week's return match, but Arsenal cannot afford to turn focus to that huge tie just yet. The race for a top-four spot in the Premier League remains wide open, though defeat to the Red Devils on Sunday and their aspirations of competing in the Champions League next season will be left in tatters.
Last weekend's 1-1 draw at Wembley Stadium was a positive result on the face of it for Arsenal, who will rightly feel they deserved more out of the match.
If not for some questionable refereeing decisions, and a poor late spot kick from Pierre-Emerick Aubameyang, the Gunners would be heading into this crucial showdown with United above their opponents in fourth.
As it is, a second defeat to their arch-rivals in the space of six weeks will lead to questions being asked of Emery, who now faces a trophiless campaign in his maiden season on these shores, on top of missing out on the top four.
Alternatively, victory this weekend and Arsenal will be considered many peoples' favourites to go on and finish fourth, while at the same time giving them momentum heading into the return match with Rennes next week.
Arsenal have won their last eight Premier League home games - they last won nine in a row within the same season at the Emirates back in 2014-15 - but they did lose 3-1 to United in the FA Cup fourth round at the end of January.
Only on two previous occasions have they lost at home to a single opponent more than once in a season - against Nottingham Forest in 1987-88 and Aston Villa in 1993-94.
This really is a massive match for Emery and his players, then, knowing that the outcome of the game could easily define how the Spaniard's first season in North London will be defined.
Recent form in Premier League: WLWWWD
Recent form (all competitions): LWWWDL
Rewind just a few months to December when the sides last faced off in the league and the mood around both clubs was significantly different. Arsenal headed into the match on a 19-game unbeaten run, whereas United were badly out of sorts.
The draw ultimately was not enough to save Jose Mourinho, though, as he was gone two weeks later following defeats to Valencia and Liverpool. United's transformation since then has been nothing short of remarkable, and that is all thanks to Solskjaer.
United were eight points behind Arsenal and 11 behind fourth-placed Chelsea when Solskjaer was brought in as Mourinho's successor a week before Christmas.
They now occupy the final Champions League qualification berth, one point better off than Arsenal and two in front of Chelsea, who have a game in hand to play.
It is not just in the Premier League that Solskjaer's magic has been felt, though, as he has also guided United into the last eight of the FA Cup - beating Arsenal at the Emirates Stadium en route - and through to the same stage of the Champions League.
If the permanent job was not already his, Wednesday's famous comeback win over Paris Saint-Germain will ensure that it is now.
The calls for Solskjaer to be handed the full-time job have grown louder and louder with each passing game, and even the players - Romelu Lukaku, Luke Shaw and Ander Herrera among them - have given their full backing to the Norwegian.
In total, Solskjaer has won 14 of his 17 matches in charge, losing just one of those - even that, at home to PSG, ultimately did not matter in hindsight as the Red Devils picked up a famous 3-1 victory at the Parc des Princes in the return leg.
In the Premier League, United are on the current longest unbeaten run in the division as they last tasted defeat 12 games ago against Liverpool, collecting 32 points from a possible 36 since then.
They have won their last six away games in the top flight and are now looking for a seventh on the spin for the first time since August 1993. Accounting for the FA Cup and Champions League, it is nine wins in a row away from Old Trafford.
Now comes another big test for Solskjaer and his men. On the basis of their previous big away tests, all passed with flying colours, you would not bet against their extraordinary run continuing this weekend.
Recent form in Premier League: DWWDWW
Recent form (all competitions): LWDWWW
Solskjaer was without nearly a whole starting lineup of players for the midweek trip to Paris, but he has been handed a big fitness boost ahead of Sunday's trip to the English capital.
Martial, who has already scored twice against Arsenal this season, is expected to make his return to action following a month on the sidelines. However, it is unlikely that the French forward will be fit enough to start.
Paul Pogba may be the only one of United's 10 midweek absentees to return, in fact, as his European ban does not carry over and he is therefore eligible to play on Sunday.
In terms of the home side, battling midfielder Lucas Torreira had his three-match suspension for last week's sending-off at Tottenham upheld, so he will sit this one out.
Danny Welbeck, Rob Holding and Hector Bellerin are all out for the rest of the season, meanwhile, but Sokratis Papastathopoulos is available despite being dismissed against Rennes in the Europa League.
Emery has already hinted that he will start Alexandre Lacazette through the middle due to the Frenchman being ruled out of European action through suspension, meaning that Aubameyang is likely to take up a place on the bench for the second league game running.
Lacazette is looking to become only the second Arsenal player to score in six consecutive home Premier League games after Thierry Henry, who did so twice (six in August 2000, seven in October 2004).
Arsenal possible starting lineup:
Leno; Maitland-Niles, Sokratis, Koscielny, Kolasinac; Guendouzi, Xhaka; Mkhitaryan, Ramsey, Iwobi; Lacazette
Manchester United possible starting lineup:
De Gea; Young, Smalling, Lindelof, Shaw; Fred, McTominay, Pogba; Pereira; Lukaku, Rashford
Head To Head
Arsenal have won two of their last three Premier League home games against Man United, losing the other, which is as many as they had managed in their previous eight.
The Red Devils were 3-1 winners the last time the sides faced off at the Emirates Stadium in the league, though, and they are now seeking back-to-back away league victories in this fixture for the first time since the mid-1980s.
Nine of Arsenal's 13 Premier League victories over United have been in games played on a Sunday.
We say: Arsenal 1-3 Manchester United
Arsenal have been in near-identical form to United over the past six Premier League matches, but going further back the Red Devils have been considerably more consistent than their opponents in all competitions, racking up victories away to the likes of Chelsea, Tottenham, PSG and indeed the Gunners. Solskjaer has a chance to become the first Man United manager in history to win his first two away meetings with Arsenal in all competitions following the Red Devils' 3-1 win at the Emirates in the FA Cup in January, and we are backing the same scoreline this weekend.