They are the ninth Italian club to win honours on the continent and they did it the hard way, seeing off the Bundesliga champions in the final - a team that had gone 51 games unbeaten across all competitions until tonight.
The man to break the run is Gian Piero Gasperini. In charge since 2016, he is the longest-serving manager with the club from Bergamo and this trophy is his first with this side.
The run to the title saw them knock out some big names just to make it to Dublin.
They topped Group D with 14 points after four wins and two draws from six games, three points ahead of Sporting.
They would face the Portuguese side again in the round of 16, and once again they saw them off with relative ease, drawing 1-1 in the first leg in Lisbon, before winning the second leg 2-1.
Their biggest test of the competition came in the quarter-finals, where they faced English giants Liverpool. The first leg at Anfield saw all of Europe sit up and pay attention to Atalanta. The Italian side won 3-0 thanks to two goals from striker Gianluca Scamacca and another from Mario Pasalic to shock Liverpool and everyone on the continent.
Liverpool did win the return match 1-0 a week later, but they could do nothing to prevent Atalanta from moving on.
That second leg was the only game in the competition they had failed to score in and that run continued in the semi-finals as a brilliant performance against Marseille after a 1-1 draw in France, saw Atalanta book their spot in the final thanks to another 3-0 win.
They carried that form into the final and made history in Dublin.
It has been a season to remember for Atalanta. Not only have they lifted the Europa League trophy, but they also reached the Coppa Italia final - losing 1-0 to Juventus - and they look set to finish fifth in Serie A.
That league position, as well as the Europa League triumph, sees them back into the Champions League for the first time since 2020. How far can Gasperini take this side next season?
‘Neverlusen’ finally beaten
The incredible season of Bayer Leverkusen finally witnessed defeat, but despite their first loss in 52 games, Xabi Alonso and his players still have much to celebrate, and much to play for.
The record of 51 games unbeaten across all competitions broke the record of Benfica from the 1950s as they won their first Bundesliga in style. No defeats in 34 games was a first in the German top flight and in the process, they were able to dethrone Bayern Munich at the top of the table.
There could yet be more domestic glory for Leverkusen on the weekend as they contest the DFB-Pokal final against second-division Kaiserslautern. If they win that game, one where they are massive favourites, they will complete an unbeaten domestic double like few have seen in European football history.