The organisation issued a statement on Friday which revealed an independent three person Anti-Doping Review Board had unanimously recommended going ahead with legal proceedings.
An arbitration panel will now rule on the case.
A statement from USADA CEO Travis T Tygart said: "USADA can confirm that the independent three person Anti-Doping Review Board (ADRB) has conducted a full evaluation and has made a unanimous recommendation to move forward with the adjudication process in accordance with the rules.
"All respondents will have the opportunity to exercise their right to a full public arbitration hearing, should they so choose, where all evidence would be presented, witness testimony would be given under oath, and an independent group of arbitrators would ultimately decide the outcome of the case.
"USADA will continue to follow the established procedures that are compliant with federal law and were approved by athletes, the US Olympic Committee, and all Olympic sports organisations."
Armstrong, 40, has always strenuously denied all allegations of doping and reacted angrily when the USADA initiated legal proceedings over "allegations of anti-doping rule violations" during his time with the United States Postal Service (USPS) cycling team. He said the agency were dredging up discredited accusations.
Armstrong survived testicular cancer early in his career and went on to win seven consecutive Tour de France titles from 1999 to 2005 while competing for the US Postal Service team and the Discovery Channel team.
He retired after the 2005 Tour de France, but returned in 2009, riding for Astana Cycling and RadioShack before retiring for a second time in February 2011, taking up triathlon earlier this year.