Agents swarmed Solyndra Thursday on the heels of last week's filing.
In addition to the bankruptcy, the solar firm also announced it was laying off 1,100 workers.
An FBI spokesperson would only say the agency executed multiple search warrants.
The money Solyndra borrowed was part of the economic stimulus package passed by Congress in 2009.
Republicans are using Solyndra's financial woes as ammunition in attacking the effectiveness of the stimulus package. The raid Thursday morning came just hours before the president appears before both chambers of Congress to appeal for more legislation that would help the economy and reduce the nation's 9.1 percent unemployment rate.
"The FBI raid further underscores that Solyndra was a bad bet from the beginning and put taxpayers at unnecessary risk," said top Republican leaders on the House Energy and Commerce Committee, Reps. Fred Upton of Michigan and Cliff Stearns of Florida, in a joint statement
Solyndra, like other companies in the nation's solar energy industry, faced declining prices for solar panels, in part because of heavy competition from Chinese companies.
The Associated Press contributed to this report.