Billionaire hedge fund manager Paul Tudor Jones said Tuesday stocks that performed the best since the depth of the pandemic are going to have a rough time as the Federal Reserve embarks on its tightening cycle.

"Clearly all the inflation trades of the pandemic are going to be challenged right now," Jones said Tuesday on CNBC's "Squawk Box." "I think it's going to be tough sledding for the inflation trades of the pandemic going forward... Things that performed the best since March 2020 are probably going to perform the worst as we go through this tightening cycle."

The central bank has signaled it could become even more aggressive than expected about tightening policy to tame down surging inflation. Central bankers including chairman Jerome Powell indicated that they expect to hike rates and taper asset purchases soon, adding they could be gearing up to reduce their balance sheet.

"He's got a lot of catching up to do. We are getting ready to see a major shift and it's going to have a lot of consequences for a variety of asset prices," Jones said.

The Fed's hawkish pivot triggered a big sell-off last week in growth-oriented technology stocks, as investors weighed the risk of rising rates.

"The real trick here would be, can the Fed unwind what many consider a financial bubble without there being huge negative economic consequences. We'll watch and see," Jones said.

Jones believes commodities could outperform in the new regime.

"Commodities relative to financial assets are so incredibly undervalued. One would think on a relative basis as we go through this tightening [cycle], commodities would outperform financial assets by a wide margin," Jones said.

Jones is the founder and chief investment officer of Tudor Investment Corp. He shot to fame after he predicted and profited from the 1987 stock market crash.

He is also the chairman of nonprofit Just Capital, which ranks public U.S. companies based on social and environmental metrics.