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The Giallorosse went behind early at Stadio Tre Fontane and never really recovered, as second half goals from Atalanta forward Maegan Kelly ended up sealing the game.
Betty Bavagnoli's side looked dangerous at times - Agnese Bonfantini in particular was always threatening - but struggled to create clear-cut opportunities.
The result means the Giallorosse still have a lot of work to do to confirm a top-four finish in their first-ever season in Serie A. They face AC Milan on Wednesday.
“Maybe 3-0 is a bit harsh on us, but we did not perform the way the coach asked us to out there,” said defender Federica Di Criscio.
“We pushed forward looking for an equaliser and in the end we conceded two more. On Wednesday we will try to bounce back, despite today’s disappointment we have shown before we are able to reset and improve – and we’ll try to do that against Milan.”
Bavagnoli's options were somewhat limited by ongoing injuries and absences to the side - but conceding an opening goal after just nine minutes also fundamentally changed a game that was always likely to be hard-fought.
“My compliments to Atalanta, they played the game the way they wanted to and did well," Bavagnoli said.
"We need to look at why we were not at it today. Once again we gifted them a goal at home, and that changed the course of the game.”
See more photos from the match in the gallery below.
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