Iwu was re-arraigned on four counts before Justice Nicholas Oweibo of the Federal High Court in Lagos.
He had earlier been arraigned in August before Justice Chuka Obiozor of the same court.
His re-arraignment on Thursday followed the transfer of the case from Justice Obiozor to Justice Oweibo.
In the charges, the EFCC alleged that Iwu committed the offence in the build-up to the 2015 general elections in which President Muhammadu Buhari defeated then-incumbent President Goodluck Jonathan.
According to the EFCC, Iwu, between December 2014 and March 27, 2015, aided the concealment of N1.23bn in the account of Bioresources Institute of Nigeria Limited with number 1018603119, domiciled in the United Bank for Africa.
The EFCC said Iwu ought to have reasonably known that the N1.23bn formed part of the proceeds of an unlawful act, to wit: fraud.
The prosecution for the EFCC, Mr Rotimi Oyedepo, told the court that the ex-INEC chairman acted contrary to sections 18(a) and 15 (2) (a) of the Money Laundering ((Prohibition) Act 2011 and was liable to be punished under Section 15(3) of the same Act.
But the defendant pleaded not guilty to the charges.
Justice Oweibo permitted him to continue on the N1bn bail earlier granted him by Justice Obiozor.
He adjourned till November 25, 2019, for the commencement of trial.