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The 44-year-old took over in June 2016 leading the promoted side from Calabria in their maiden Serie A campaign.
They dramatically survived last season by finishing 17th but this season are just one place higher with 12 points from 15 games.
“It’s all true, I’ve made my decision and I’m not going back on it,” Nicola had told Gazzetta dello Sport earlier in the day.
The club later confirmed that he had handed in his notice along with his coaching staff.
Crotone are coming off four consecutive defeats in Serie A and the Italian Cup.
According to Italian media Nicola had a disagreement with club bosses after Monday’s 3-0 league defeat to Udinese.
Nicola famously kept his promise to fans after avoiding relegation on the final day of last season by cycling 1,300 km from Crotone in the ‘sole’ of Italy to his hometown of Turin.
It was also to raise awareness for road safety after his son was killed four years ago in a road accident while riding a bicycle.
Former Crotone coach Massimo Drago has been touted as a possible successor.
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