Currently on loan at AC Milan, the Frenchman had hoped to find a new club with the Rossoneri unwilling to play him as it would trigger an automatic £12million purchase option.
Bakayoko, 28, remains under contract at Stamford Bridge for another 18 months.
Serie A club Cremonese and Lyon of Ligue 1 had both been in talks with the player over signing him for the rest of the season.
But agent Federico Pastorello has confirmed that neither move is expected to be completed after encountering “problems” on deadline day.
“Bakayoko couldn’t join Cremonese due to a few issues,” he told Sky Sport Italia.
“I don’t think [he’ll join Lyon]. There are some problems between Lyon, Milan and Chelsea.”
Chelsea are hoping to bolster their midfield in the final hours of the transfer window with talks ongoing between the Blues and Benfica over Enzo Fernandez.
Jorginho is set to depart the squad as a loan switch to Arsenal nears completion.