Flora Tallinn, Valletta and The New Saints all earned narrow first-leg wins as the first eight teams set off on the road to Cardiff, venue for the 2017 UEFA Champions League final.
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Flora Tallinn 2-1 Lincoln (Alliku 35, Sappinen 49; J Chipolina 57)
Estonian champions Flora will look to defend a slender lead in the second leg in Gibraltar thanks to a goal either side of half-time, Joseph Chipolina giving Lincoln hope just before the hour.
Second leg: Wednesday 6 July, 19:00CEST
The New Saints 2-1 Tre Penne (Quigley 13, Mullan 40; Fraternali 16)
Welsh title holders The New Saints enjoyed the lion's share of the chances in Oswestry but could only establish a one-goal lead advantage for the second leg, Jamie Mullan getting what could prove a crucial goal before the break.
Second leg: Tuesday 5 July, 20:30CEST
Valletta 1-0 B36 Tórshavn (Falcone 69)
Federico Falcone made the difference for the Maltese champions as their second-half pressure finally paid off, leaving B36 with work to do in Torshavn next week.
Second leg: Tuesday 5 July, 19:00CEST
Santa Coloma 0-0 Alashkert
Both teams will fancy their chances in Armenia next Tuesday after neither side was able make the breakthrough at the Estadi Comunal.
Second leg: Tuesday 5 July, 17:00CEST