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Ennis-Hill, 30, hinted at retirement after narrowly losing her heptathlon title to 21-year-old Belgian Nafissatou Thiam in a thrilling contest in Rio.
Minichiello told the BBC she should "take two or three months and work out exactly what you do want to do" .
"When she takes that time and makes that decision we'll move from there."
Next year the World Championships come to London, where Ennis-Hill won Olympic gold four years ago, but after missing out on retaining her title by 35 points, the Sheffield athlete would not commit to continuing.
"It's going to be a tough decision, I'm going to go away and think about it," she said. "At this moment, I'm tired and emotional - it's a big decision."
Minichiello has coached Ennis-Hill since she was 13, helping her become world champion in 2009, Olympic champion in London three years later, and then take gold at the 2015 World Championships just 14 months after she gave birth to her son Reggie.
The Sheffield-born coach said it might be time for him to "be selfish", should Ennis-Hill retire.
"She clearly won't do another Olympic Games in 2020. If there are opportunities coming up, I need to start having a look at that as a career going forwards," he continued.
"It will be a bit of a decision I have to make for myself so maybe it's time for me to be a bit selfish and make some choices for me."
Minichiello said that he counted Ennis-Hill's silver in Rio as a "better performance" than her gold at London 2012, but he had "mixed emotions" after the event.
"If you look at the progress she's made, having missed two years of heptathlon competition to come back, the progress she's made is pretty remarkable," he added.
Britain's Olympic silver medallist Jessica Ennis-Hill should "take time" to consider her future, her coach Toni Minichiello has said.