Razwan Faraz, former deputy head teacher at Nansen Primary, also, on one occasion, had girls sitting at the back and boys at the front, it was claimed.
Mr Faraz and four other senior staff deny unacceptable professional conduct.
The school was investigated amid claims of a Muslim hardliners' plot to control several schools.
The National College for Teaching and Leadership hearing, in Coventry, heard from former staff member Hilary Thompson, who resigned in May 2013 because of "ongoing exclusion, isolation, lies and bullying."
The hearing was told her resignation followed periods of absence for sickness and came after a leadership restructure at Park View Educational Trust.
The trust ran Park View Academy, Nansen Primary and Golden Hillock Primary.
In her witness statement, Mrs Thompson said the Islamic assemblies were held without consultation with the head teacher at the time or parents.
On one occasion the children were segregated and appeared to be chanting "Islamic prayer".
Some of the assemblies, she said, were lead by Monzoor "Moz" Hussain, former head teacher at Park View Academy.
Some witnesses have been granted anonymity when giving evidence in the hearing.
A senior teacher at Park View, known as "Witness A", told the hearing she was aware of flyers being distributed saying things such as women should obey their husbands in marriage.
She said prefects were acting as monitors and reporting back to some teachers when boys and girls were getting too close.
Where dating was evident, some children were segregated and kept in silence.
The tribunal was also told that in her witness statement she told of hearing both pupils and staff use anti-Semitic language.
She said it went on unchallenged and "racist and homophobic comments were an on-going problem" at Park View Academy.
Staff before the tribunal are accused of unprofessional conduct, by agreeing to the inclusion of an undue amount of religious influence in the education of pupils along with. They are:
In a separate hearing, in Birmingham, teacher Johirul Islam had an accusation of bringing undue religious influence into lessons dismissed.
Another hearing, in Solihull, against Inamulhuq Anwar and Akeel Ahmed has finished. The panel has adjourned to consider its conclusion, which will be delivered at a later date.
Ten teachers in total face hearings.

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Morgan's men are through to the semi-finals after beating New Zealand, but have the chance to put Australia out.
"If we're going to be contenders, we need to beat the best and Australia are one of the best," said Morgan.
"So to go in to a game like that with no other attitude than winning is very important to us."
England will go through to the semis as Group A winners regardless of the result against Australia, but Saturday's clash could be the final time the two sides meet before this winter's Ashes series.
New Zealand will also be looking for England to do them a favour, as an Australia win would send the Kiwis out.
In Cardiff on Tuesday, England posted 310 and looked under pressure when New Zealand reached 158-2.
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But after Mark Wood found extra bounce to remove Black Caps skipper Kane Williamson for 87, it began a collapse that saw New Zealand lose their last eight wickets for 65 runs.
"We batted OK," said Morgan. "We weren't that pleased at halfway and thought we were maybe 20 or 30 short of par.
"The guys did the right things, but it doesn't always work. But, when you post over 300 you're always in with a shout."
In an all-round display from the England side, four of the batsmen made scores in excess of 48, while all five bowlers used took at least one wicket.
However, the form of opener Jason Roy remains a concern. The Surrey man, who had not passed 20 in his previous seven ODIs, made 13 before being bowled by Adam Milne.
Morgan, who has previously backed Roy to remain in the England side throughout the tournament, said: "It doesn't change very much.
"We'll obviously have a chat about the team, but, certainly within a winning side, it's very hard to make changes going into a game where you don't really have much to lose."
Islamic assemblies were held without consultation at a Birmingham school involved in the "Trojan Horse" affair, a misconduct panel has heard.
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England captain Eoin Morgan says his side will show no let-up when they meet Australia in the Champions Trophy at Edgbaston on Saturday.