Ironically it was ill-discipline that nearly cost them dear in the end, the dismissal in the first round of top scorer Diafra Sakho robbing them of a goal threat before James Tomkins' sending off on the night as the Hammers slumped to a 1-0 defeat to draw the game 1-1 on aggregate.
Slaven Bilic's side were nearly made to pay the price for their slender 1-0 win against Birkirkara FC at the Boleyn Ground last week teeing them up for a potentially tricky their trip to Malta for tonight's reverse fixture.
Somehow they produced an even worse performance but managed to avoid an embarrassing early exit from the competition by putting away all their penalties to win the shootout 5-4.
There will inevitably be much tougher tests to come, but what did we learn from the game?
1) Lack of discipline could cost West Ham dear this season
In both of West Ham's Europa League away matches they have seen a key player sent off. In the last round against Lusitanos top scorer Diafra Sakho saw red for an altercation with a defender.
Then tonight away at Maltese minnows Birkirkara, James Tomkins was given his marching orders to leave his side staring a potentially embarrassing early exit in the face.
You could argue both dismissals were harsh but the players would have been well drilled on what to expect from the European referees. Ironically the Hammers had only qualified for this season's competition through the FIFA Fair Play standings. But their lack of game sense nearly cost them dear.
2) Kevin Nolan should not have a future at West Ham
Nolan has been a great servant for the Hammers over the last four years. But his time, like Sam Allardyce before him, has come to a natural conclusion. Still the club captain, Nolan was one of the worst players on the pitch against Birkirkara. Slow, even pedestrian at times, ponderous on the ball and constantly gave away possession. Looking at the two sides based on tonight's performance it would have been difficult to argue that Nolan would get in Birkirkara's side he was that bad. He was withdrawn after just 58 minutes which tells its own story. If Bilic plans to keep him as a squad player, he must address the captaincy issue as soon as possible. But a clean break would be best for all concerned.
3) It is clear why Bilic pushed the boat out to sign Ogbonna
A distinct lack of pace in West Ham's side, particularly at the back, was all too evident against Birkirkara. James Collins and James Tomkins were paired together at the back with Winston Reid withdrawing before kick-off due to a minor injury. Many fans were surprised to see Bilic splash out over £8 million on Juventus defender Angelo Ogbonna given they have Tomkins, Collins, Reid, Doneil Henry and Reece Burke in their ranks with a number of other young players emerging.
But the lack of pace was exposed by the Maltese minnows all evening, particularly for Fabrizio Miccoli's goal on 14 minutes. Ogbonna and Reid will undoubtedly be the first choice pairing.
4) West Ham don't just need one new striker, they need two
Some West Ham fans were glad to see forgotten striker Mauro Zarate return to the club with a clean slate this season. But he has done little so far to prove Sam Allardyce was wrong to freeze him out. Holds on to the ball far too long often losing it, has had very little impact on any of the games he has played so far and was upstaged by Birkirkara's 36-year-old former Italy international Fabrizio Miccoli. In desperation Bilic sent on Modibo Maiga for yet another chance to show he has a future at West Ham. But if Zarate was poor, Maiga was awful. Constantly gave the ball away and did everything half-heartedly. To be fair neither striker had anything to feed off, but they did little to try and create space and opportunities. The Hammers are in the hunt for a new striker but on this evidence, and with the injury-prone Andy Carroll out until at least September, they will need two.
5) Slaven Bilic is going to need time to change West Ham's style
Under Sam Allardyce the Hammers played a certain style. It was a style that got results and did the job. But it was also a style which ultimately cost him his job as Hammers fans grew fed up towards the end of his four-year tenure. Bilic was going to change all that, play bright, inventive attacking football on the floor more in tune with the 'West Ham way'. What West Ham produced over two legs against Birkirkara was none of those things. But the former Croatia and Besiktas boss has only been in the job less than a month and will need to be given time to implement such a contrasting style and mentality in his team. He has the charisma and CV to do it but performances like tonight's will ramp up some unwelcome pressure.