Along with prospects of lower yields, those farmers will have to take more time to harvest as they slowly move equipment through fields to try and scoop up crops knocked down by the tempest. And that means farmers have to spend more money on fuel to keep combines in the fields longer.
"The timing was devastating," said Mike Smith, an agricultural extension agent in Henderson County in western Kentucky. "It's changed the whole complexion of this year's harvest."
Smith predicted wind damage would lower some corn yields as much as 20 percent in the county.
Elsewhere, some Midwest crops received a needed soaking.
Heavy rains in central and northern Illinois came too late to help the state's corn crop but could give a late boost for soybeans after an extended summer dry spell, said Darrel Good, a professor of agricultural economics at the University of Illinois.
"Since the bean crop is pretty late maturing this year, it probably has some overall beneficial effects," he said.
But in western Kentucky, Ike lashed corn fields with high winds. Farmer Jerry Griffith said damage from Sunday's storm was considerable, with up to 90 percent of stalks battered to the ground in some fields.
"It's hit us a pretty good blow," the Graves County farmer said during a break from harvesting corn. "We're able to pick up some of that corn, but we can't get all of it."
He had about 600 acres of unharvested corn when Ike struck, about half his crop.
Bill Sutherly, who grows about 2,000 acres of corn, soybeans and hay near Troy in western Ohio, estimates the wind damaged up to 15 percent of his corn. He said harvesting his crop will take longer as he slows the combines to try to get under flattened stalks and salvage some corn.
"We're going to use more fuel," Sutherly said.
In Texas, where Ike made landfall as a Category 2 hurricane, strong winds and rains heavily damaged the rice crop, equipment and storage facilities east of Houston.
The storm was blamed for killing about 4,000 cattle in two southeast Texas counties and some of the missing livestock may never be found.
"They're being eaten by alligators," said Kathleen Phillips of the Texas AgriLife Extension Service.
About a quarter of Arkansas' rice crop was affected by wind and rain from remnants of hurricanes Ike and Gustav. Based on preliminary reports, farmers could lose 10 percent of their overall yield because of the storms, said Chuck Wilson, a rice expert at the University of Arkansas Cooperative Extension Service.
Some rice was blown down but can still be harvested, though it won't be cheap or easy.
"The biggest problem is it slows everything down, so it becomes very costly to harvest," Wilson said.
The rice harvest in Arkansas began later this year after a cold, wet spring delayed planting.
"We were set for a pretty good crop," said Craighead County extension agent Steve Culp. "I'm sure this will have an impact."
Elsewhere, Ike flooded some rice belt parishes in southwestern Louisiana. Though there was only a small amount of rice in the fields, some growers will still feel the sting.
"For some farmers, it might be their entire crop," said Steven Linscombe, director of the LSU AgCenter's Rice Research Station in Rayne. "We have some farmers who plant late after crawfish production."
Corn flattened in Indiana likely won't recover and will make for a difficult harvest, said Tony Vyn, a Purdue University agronomy professor. He said he couldn't comment on the extent of the damage, however.
Ike's remnants dealt only a glancing blow to other areas.
Corn and soybeans were soaked by up to a foot of rain as Ike barreled through central and northern Illinois, but the timing wasn't so bad because crops were mature, University of Illinois agriculture professor Emerson Nafziger said.
"In July this would have been a much bigger problem," he added.
Nafziger said serious losses should be limited to fields near flooded streams and rivers - a tiny fraction of the crop.
Elsewhere, heavy rain actually helped parts of southern and southeastern Iowa in need of moisture, producing "significant surpluses" in topsoil moisture, according to the USDA's National Agricultural Statistics Service Iowa field office.
In western Kentucky, several dark-fired tobacco growers lost barns to wind-fanned fires.
Meanwhile, the winds damaged some orchards.
Bill Dodd, president of the Ohio Fruit Growers Marketing Association, estimates that 5 percent of Ohio's apple crop was damaged - both from falling apples and from fruit banging together or against branches.
Dan Simmons, owner of Peace Valley Orchard near Youngstown, lost 10,000 to 12,000 bushels of apples - almost 15 percent of his crop - and up to 200 of his 39,000 fruit trees.
"Does it hurt? Very deeply," he said. "But it's not devastating."