By the time she retired from the Court in 1978, Muñoz-Palma had become identified, along with Claudio Teehankee, as a dissenter from rulings that affirmed the decrees and actions enforced by her appointer, President Ferdinand Marcos, during his martial law rule. As early as 1975, she had expressed skepticism that "a referendum under martial rule can be of no far-reaching significance as it is accomplished under an atmosphere or climate of fear." The following year, she voted against allowing Marcos the right to propose amendments to the Constitution by himself, and in doing so, ventured to call for the lifting of martial law itself. In a later dissent, she added that "under a martial law regime there is, undeniably, repression of certain rights and freedoms, and any opinion expressed would not pass the test of a free and untrammeled expression of the will of the people. That "artial law connotes power of the gun, meant coercion by the military, and compulsion and intimidation" was so stated by President Ferdinand E. Marcos upon proclamation of martial law in the country."
Opposition against Marcos
After her retirement from the Court, Muñoz-Palma emerged as a prominent figure in the anti-Marcos political opposition. In 1984, she was elected under the UNIDO banner to the Regular Batasang Pambansa as an Assemblywoman, repenting Quezon City. She headed for a time a National Unification Council that sought to unify all anti-Marcos opposition groups. She also became an early supporter of the attempt to draft the then-reluctant Corazon Aquino to run for the presidency against Marcos.
1986 Constitutional Commission and later life
After Aquino assumed the presidency in 1986, Muñoz-Palma called in vain for the retention of the unicameral Batasang Pambansa as the country's legislative body but such plea was not heeded by the new President. Instead, the President dissolved it by means of a proclamation, which formed a provisional constitution that declares her government to be revolutionary and assumed legislative powers the now former Batasan held. When Aquino created the 1986 Constitutional Commission to draft the new Constitution, she appointed Muñoz-Palma as one of its members. The Commission would later elect her as its Chairwoman. Following the ratification of the 1987 Constitution, Muñoz-Palma faded from the public eye. However, in 1998, she supported Vice-President Joseph Estrada for the presidency. After his election, President Estrada appointed the 85-year-old Muñoz-Palma as Chairperson of the Philippine Charity Sweepstakes Office. She served in this capacity until 2000. Muñoz-Palma strongly denounced the circumstances that led to Estrada's vacation of the presidency and the assumption into office of Gloria Macapagal-Arroyo. Muñoz-Palma died on January 2, 2006, at the age of 92.
Legacy
Three years later, the International Women’s Forum inducted her into its International Hall of Fame. Her family and friends formed the Justice Cecilia Muñoz Palma Foundation to “continue what she started,” and will be launched on February 2009. A street beside the City Hall of Manila was named in her memory.