A probe was ordered by the police watchdog after concern over the stop of the athlete, then 27, and her partner Ricardo dos Santos in Maida Vale in July 2020.
The couple accused the force of “racial profiling” when they were handcuffed and separated from their three-month-old son during the stop.
Mr dos Santos, a Portuguese 400m sprinter who competed at the Tokyo 2020 Olympics, was searched for weapons and for drugs and Ms Williams for weapons. Nothing was found.
On Monday, five officers appeared at a police misconduct hearing in south east London.
Disciplinary panel chairman Chew Yin Jones asked each of them: “Do you accept or deny that your behaviour on July 4 2020 amounted to gross misconduct?”
Each of the officers replied with the word “deny”. Gross misconduct is the most serious disciplinary charge the officers can face and, if proven, they could be sacked.
Acting Sergeant Rachel Simpson and Pcs Allan Casey, Jonathan Clapham, Michael Bond and Sam Franks all face allegations that they breached police standards over equality and diversity during the stop-and-search.
Acting Sgt Simpson and Pcs Clapham, Bond and Franks also face allegations that their actions amounted to a breach of professional behaviour standards in relation to the use of force.
They are said to have failed in relation to their levels of authority, respect and courtesy as well as in their duties and responsibilities.
Pc Casey is also accused of breaching professional standards in the way he carried out his duties and responsibilities or gave orders and instructions.
It is also alleged that the honesty and integrity of Pcs Casey, Clapham, Bond and Franks also breached professional behaviour standards.
Footage of the search was widely shared on social media. Both Ms Williams, 29, and Mr Dos Santos, 28, have been critical of how they were treated.
In a previous statement, the couple welcomed the misconduct hearing.
Ms Williams said she hoped the hearings open “the door for the Met to start being more honest and reflective about the culture of racism which is undoubtedly still a reality within the organisation.”
Mr dos Santos added: “This has been a long journey, and one which has not been easy.
“This sheds a light on how difficult it is to ensure the police are held responsible for their failings.”
The Met’s internal Directorate of Professional Standards carried out two reviews, which found no misconduct by any officers, before misconduct hearings were ordered by the police watchdog.
The then Met commissioner, Cressida Dick, claimed that “any officer worth their salt would have stopped that car" and that she did not “personally accept” footage of the stop "reveals racism".
However, senior officers in the force have previously apologised for “the distress that this incident clearly caused Ms Williams and Mr dos Santos.”