The 23-year-old French rider claimed her first gold medal in a senior major event following the U23 continental title she won two years ago in Monteceneri, Switzerland.
"A major competition like a world or European championships is always different, because there's a jersey at stake and you can wear it for all of next season," the newly crowned champion said after the race said after the race.
Having claimed two World cup events this season on top of a second straight national title, she will be the favourite for next week's World Championships in Les Gets, less than one hour from her hometown Annecy.
"I hope to be able to ride for the medals again. I did the work, I prepared well, so we will see.”
Lecomte shared the podium with teammate Pauline Ferrand-Prevot, who took silver after suffering a mechanical on lap three of seven while leading the race. Anne Terpstra of the Netherlands claimed bronze.
Serious wet conditions represented an extra challenge for the competitors, who had to ride approximately 30 km across the purpose-built 4.27km-course at the Olympiapark seven times after a 1km start loop.
Lecomte and Ferrand-Prevot immediately jumped to the front of the pack and built a 30-second lead on Swiss duo Jolanda Neff and Alessandra Keller.
On lap two three-time world champion Ferrand-Prevot went solo and looked like she would sail to a third straight European title but bad luck struck as her chain went off the chainring and cost her more than a minute.
By the time she managed to get the muddy chain back on again, she was 43 seconds behind Lecomte, who held her lead until the end to cross the finish line in one hour 28 minutes and four seconds.
"Loana passed me. I had a one minute gap (behind Lecomte), so I tried to close the gap, but I think it was impossible,” said the silver medallist
Ferrand-Prevot followed 37 seconds later, hugging her teammate, with Terpstra over three minutes behind the winner. Olympic champion Neff was fourth, a further 30 seconds back.