The 19-commodity Thomson Reuters-Jefferies CRB index fell 0.4 percent to its lowest levels since June 29, 2012, even though oil prices rose, tracking the stock market's rally.
The CRB fell as the dollar jumped to a three-week high against the euro after European Central Bank President Mario Draghi spoke about downside risks to euro zone growth. Most commodities are priced in the dollar and gains in the currency add to ownership costs for such raw materials.
Gold slumped to its lowest price in nearly three years as the rally in US equity markets further cut into demand for bullion as a hedge against economic uncertainty.
The spot price of gold hit its lowest since August 2010, reaching $1,223.54 an ounce. It was down 4 percent at $1,225.64 an ounce by 5:00 p.m. EDT (2100 GMT).
With two sessions left in the second quarter, gold was down 23 percent for the period, on course for its biggest quarterly decline since Reuters began tracking such moves in 1968.
Silver prices dropped 5 percent. Platinum group metals also declined sharply.
Copper slipped on concerns about demand from China, after the central bank in the top copper-consuming country failed to fully reassure investors fearing a credit crunch.
Benchmark copper on the London Metal Exchange closed at $6,735 per tonne, down 1 percent down from Tuesday's close.
In coffee, futures for premium grade arabica beans fell to just above recent multi-year lows, on pressure from the stronger dollar. New York-traded arabica for September closed down $2.10, or about 2 percent, at $1.1845 a lb.
Oil prices edged higher after shaking off early losses caused by a large build up in US gasoline inventories.
Closely-watched Brent crude grade out of Europe's North Sea settled up 40 cents at $101.66 a barrel.