Thanks to Mother Nature, pumpkin pie may be a lot harder to come by this Thanksgiving.

Record rainfall in June created a shortage in canned pumpkin, the main ingredient in pumpkin pie. The majority of the pumpkins used by Libby, a top supplier of canned pumpkin, come from a central Illinois community that was hit hard by summer storms.

Between pumpkins, almonds and other weather-ravaged crops, you'd think the cost of a Thanksgiving dinner may be even pricier than last year, when the feast clocked in at around $49 on average. Though, the American Farm Bureau Federation's Fall Harvest Marketbasket survey out in September suggests otherwise.

"Energy prices, which affect everything in the marketbasket, have been quite a bit lower compared to a year ago. Processing, packaging, transportation and retail operations are all fairly energy-intensive," John Anderson, AFBF's deputy chief economist, told Growing Georgia. That means prices for everything from milk to vegetable oil might actually be cheaper this year. 

Still, for many crops, the weather and other freak events like the outbreak of bird flu in the U.S. are sure to play havoc on your dinner table. Such household staples as eggs and orange juice, have already seen prices rise since last year, according to the survey. 

For Libby, as much as a third of puree yields may have been washed away. The company is now carefully managing its distribution to ensure retailers across the U.S. get their share of pumpkins.

Libby's 2015 harvest is expected to last until mid-November, but once that's shipped out, pumpkin sales will cease until next year's summer harvest. 

Crop experts say there should be enough pumpkins for Halloween but advise all pumpkin pie lovers to stock up on canned pumpkin while supplies last. Or you can learn how to make your own pumpkin puree with this easy Food Network recipe.  

If you don't mind a little extra work, making a pumpkin pie from scratch might actually be the way to go this year. Even before the shortage, retailers boosted the price of canned pumpkins.