Arrested in London in August and awaiting extradition to the US, Babar Ahmad, 30, was on Wednesday also indicted for supplying fighters of the banned groups with gas masks, night-vision goggles and camouflage suits.
His indictment accuses him of supporting terrorism, conspiring to kill Americans and laundering money.
"The acts of terrorism specifically involved violence against persons, including murder, and violence against property in those countries to achieve political, religious and ideological ends," assistant US attorney Robert M.Appleton said.
Ahmad allegedly ran several sites, including Azzam.com, which US investigators say were used to funnel money to terrorists.
"Azzam Publications has been set up to propagate the call for jihad ... to incite the believers and also, secondly, to raise some money for the brothers," the website apparently said.
Ahmad allegedly recruited
fighters for Chechen separatists
The site allegedly encouraged people to train in street combat, land mine operations and sniper skills.
Financial donors were told to smuggle cash into Pakistan and pass it to the Taliban consul-general, investigators said.
"If you are supporting the Taliban and the Taliban is killing American soldiers, we are alleging you are conspiring to kill American citizens abroad," Connecticut US attorney Kevin O'Connor said.
The charges were filed in Connecticut because Ahmad allegedly used an internet service provider in the state to host one of his sites.
Ahmad said little during his August court appearance in London. When asked if he understood the charges against him, he replied: "Not really. It's all a bit confusing to me."