One of the biggest names in the second qualifying round, Sporting Braga, only managed to score once away to Zeljeznicar Pancevo as the Portuguese outfit won 1-0.
This season marks the first time in 12 years in which Braga will not feature in the Europa League at some point, and many will expect for them to go far in the Conference League.
They did not particularly impress in Serbia though, with the goal coming on one of just four attempts. They will look to do better next Thursday at home in the return leg.
Wednesday also saw Istanbul Basaksehir in action, though club from Turkey also struggled. Unlike Braga, they ended finishing on level terms in a 1-1 draw with Finnish club Inter Turku.
Clinton Jephta put the visitors ahead early on as an upset looked to potentially be on the cards. The equaliser came shortly after the restart through Emin Bayram as Basaksehir are now winless in their last three home matches in Europe.
Looking to bounce back from Champions League disappointment, Riga FC battled past Vardar 3-2 in a back-and-forth clash. Both teams led in the first half, with the North Macedonian champions restoring parity midway through the second period.
Riga scored the winner though, as Iago Siqueira's second of the game deciding the first leg. The side from the Latvian capital maintain a perfect record versus sides from North Macedonian opposition across three games.
Dinamo Minsk storm back in Azerbaijan
Despite conceding twice in the opening eight minutes, Dinamo Minsk roared back against Neftci in Baku to win 4-2.
The opener was scored less than two minutes in at the Palms Sports Arena, with the hosts doubling their lead a few minutes later. The Belarusians did come alive after that, grabbing one back before the half.
By the hour mark, the comeback was complete, thanks to goals from Evgeniy Malashevich and Karen Vardanyan. A fourth was added towards the end after Guljigit Alykulov got his own rebound from a penalty.
The result marked the first time an Azeri club lost in Europe this season after seven wins from the country's three other representatives.
Bohemians defeated Ballkani 2-1 to take a key advantage with them to Kosovo next week. Meanwhile, Spartak Trnava and CSKA 1948 Sofia played to a scoreless draw in Slovakia.
Tuesday had three games as the round commenced with an eight-goal result in Luxembourg. Atert Bissen fell 6-2 at home to Gyori ETO. Five different players got on the scoreboard for the Hungarians, who are in a solid position to progress.
FCI Levadia Tallinn will play the second leg of their tie with IFK Goteborg with a lead after beating the Swedes 2-1 on their travels. Floriana and Drita are also well poised for an exciting second leg after both sides scored in stoppage time in their 1-1 draw.
The remaining 40 first leg matches in the second qualifying round will occur on Thursday, which will feature the likes of Ajax, Partizan Belgrade, FC Kobenhavn, Rapid Wien, Austria Wien, and Gent.