Morales issued a decree allowing the takeover of shares in Empresa de Electricidad de La Paz (Electropaz) and Empresa de Luz y Fuerza de Oruro (Elfeo), which supply energy in the Andean nation.
In the ceremony at Bolivia's government palace, Morales also announced the expropriation of an investment management company and a service provider belonging to the Spanish energy giant.
Morales said he had "been forced to take this step" to ensure that electric service rates remained "equitable" in the regions of La Paz and Oruro. Soldiers guarded the installations of the electricity distribution companies, marked with signs reading: "Nationalized."
The decree read by Morales also calls for Iberdrola to receive indemnification after an independent firm is hired within 180 days to determine the value of the nationalized shares.
Telephone calls and emails seeking comment from Iberdrola in Spain were not immediately answered.
Morales in May also nationalized Transportadora de Electricidad belonging to Spanish company Red Electrica, which controlled 74 percent of energy transmission in Bolivia.
In his first year in office in 2006, the Bolivian president nationalized the oil industry through a renegotiation of contracts with a dozen oil companies, including Repsol, Petrobras, BG and Total.
In 2009 Morales transferred to state control the country's largest telephone operator, which had been controlled by Italy's ETI, and in 2010 he did the same with the four largest power generators, which had belonged to French-owned Suez, Rurelec of Britain and also to Bolivian shareholders.
Associated Press writer Harold Heckle contributed to this report from Madrid.