The Nigeria international impressed on loan at Leganes last season and has been keen on returning to the Liga club permanently where he will rank among the team’s record signings.
The Blues ultimately dropped their €7m (£6m/$8m) asking price which had scared off Celta Vigo, who explored a move for the 25-year-old before looking elsewhere.
The Madrid club are still agreeing on how to structure the payments of the deal and therefore there is still no medical set for Omeruo’s return to Leganes.
The transfer window in Spain does not close until September 2, but the club's coach Mauricio Pellegrino wants the defender in sooner ahead of the new season.
Meanwhile, Chelsea have extended Trevoh Chalobah's contract until 2022 and agreed to send their youngster out on loan for another season.
Michael Hector's future remains less certain on deadline day as there are doubts he can complete a permanent move to Sheffield Wednesday before the 5pm BST (12pm ET) cut-off point.
Chelsea remain unimpressed by Wednesday's offers to bring back the defender, who was named the Owls’ player of the season last term during his loan spell.
The Blues want to make a profit on the £4m they initially paid to sign the Jamaica international from Reading in 2015, but the Owls have not come close to reaching their valuation.
Hector has only a year left to run on his contract and there are fears that he could be spending his last season away from the pitch after talks stalled.
Chelsea have made over £100m $122m) from selling players this summer, with the departing players including the likes of Eden Hazard, Ola Aina, Tomas Kalas and Kasey Palmer.
And that number is also set to be swollen by the £8m ($10m) transfer of David Luiz to London rivals Arsenal before the transfer window closes.