The now-ex-tropical cyclone crossed Western Australia's northwest coast as a category-five system on Thursday, bringing record winds of 213km/h and damaging isolated properties.
It has since tracked towards the southern Northern Territory, but is not expected to cause significant flooding.
Pardoo Roadhouse and Tavern, 150km northeast of Port Hedland, suffered at least $4 million in damage, with accommodation and staff rooms wiped out and the roadhouse roof ripped off, letting in torrential rain and debris.
"There is a possibility that we may not be able to rebuild," manager Kelly Anne Martinez said in a Facebook post.
"We are not going to give up and we are exploring every possible avenue to fight for our roadhouse. But we need help.
"Everyone here ... desperately needs action and support from the government."
As well as tossing trees around the roadhouse grounds, Ilsa also dumped a road sign that had been stationed 5km down the highway, images posted to Facebook show.
While most staff waited out the storm from Port Hedland, a handful of staff remained on site and rode it out in a shipping container.
Elsewhere, Telfer gold mine operator Newcrest Mining has begun assessing the Pilbara site for hazards such as fallen power lines and loose tree branches as well as any hidden structural damage.
WA Fire and Emergency Services Commissioner Darren Klemm said the full extent of the destruction could take days to assess.
In the NT, a severe weather warning for residents in southern parts of the territory was lifted on Sunday morning as the system weakened.
A strong ridge would develop across the territory's south and centre and direct a surge of cooler and drier southeasterly winds into the base of the Top End, the weather bureau said.
Catchments were moderately wet following rainfall over recent weeks and months but no significant rainfall was forecast over a flood watch area for the next few days.
Flooding in low-lying areas was expected to ease. Travellers were advised to check road conditions before setting out, particularly if planning to use unsealed roads.
Residents and small businesses in Port Hedland and the shires of East Pilbara and Broome are eligible for support through the jointly-funded Commonwealth-State Disaster Recovery Funding Arrangements.
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