After crossing the coast early on Friday between De Grey and Pardoo as a category five system, Ilsa was downgraded to a category one cyclone by afternoon, as it tracked quickly through the eastern Pilbara with wind gusts of up to 170km/h.
A red alert remains for Wallal Downs on the coast and inland to Telfer, Punmu and Parnngurr.
"I wanted to just really emphasise for those communities, even though the system has crossed the coast, please remain vigilant," the Bureau of Meteorology's Todd Smith said on Friday.
"We are expecting damaging to destructive winds today and into this evening as the system continues to track towards the east."
Telfer gold mine operator Newcrest Mining said the cyclone had passed and the skeleton staff who had remained were safe and sound.
It said it would start assessing the site for hazards like fallen power lines and loose tree branches, and for any structural damage.
"Pending inspections of the airstrip and village, we aim to commence bringing the majority of people back to site from tomorrow afternoon and through the remainder of the weekend," the miner said.
Pardoo Roadhouse and Tavern bore the brunt of the category five cyclone when it crossed, packing record winds of 213km/h.
Owners of the remote stop, 151km northeast of Port Hedland, said a rebuild was planned despite the massive clean-up ahead.
"We are all still a bit shaken and emotional to see the damage from Cyclone Ilsa," they posted on Facebook.
"She may have wiped us out but she can't take away our spirit."
The owners launched a GoFundMe page to help pay for the estimated $4 million damage.
"The roof of our roadhouse is gone, staff rooms and buildings have been wiped out, most of the accommodation we offered onsite has been wiped out or received extensive damage," they wrote.
"Trees have been uprooted. Sixty to 70 per cent of the solar panels installed last year to power our whole site was blown away. And that's just the beginning."
WA Fire and Emergency Services Commissioner Darren Klemm said the damage at Pardoo was significant but it would take a couple of days to get a full picture.
"What they saw once the sun rise happened would have been devastating to them," Mr Klemm said.
"So whatever we're able to do to assist them through the insurance process or whatever else, we'll make those decisions as we know more."
The region had remain largely unscathed otherwise.
It was back to business in Port Hedland.
Australia's busiest port reopened on Friday morning after the town was spared Ilsa's wrath, with mining operations set to resume late on Friday.
Mayor Peter Carter said he was awake for most of the night, listening to howling winds which suddenly died about 1.30am.
"We dodged a major bullet," he told AAP.
The storm is expected to weaken below tropical cyclone strength on Friday night as it moves into southern parts of the Northern Territory.
Forecasters have warned communities including Alice Springs, Yulara and Ti Tree to be on alert for flash flooding and gale-force winds.
"Those really intense rain falls are going to fall over a space of few hours so there could be some flash flooding through the area, particularly the northern parts of the Lasseter district and into the northwest parts of the Simpson Desert," senior meteorologist Sally Cutter said.
Prime Minister Anthony Albanese took to Twitter to deliver a message to those affected: "Take care of yourselves, look after each other, and listen out for updates from local authorities".
The storms are expected to clear by late Saturday.
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