"We will be drastic toward those who in blind madness dare to steal the public's money," said Morales, paraphrasing a line from the country's national anthem as he was sworn in.
Those impatient for reform have signaled they intend to hold Morales to his promises to clean up government. A public protest has been called for Saturday, just two days after the inauguration, to remind the new president of his campaign slogan, "Neither corrupt nor a thief."
The new president's ability to approve new anti-graft laws will require reaching agreement with the country's more established political parties, as his center-right National Convergence Front party controls just 11 of 158 seats in the new Congress.
Morales has yet to say who will make up his Cabinet, and he already suffered one political setback when prosecutors formally asked for the equivalent of impeachment proceedings against Edgar Justino Ovalle, an allied lawmaker suspected of human rights violations dating to Guatemala's civil war.
"He is a president who takes office without a party, without well-qualified people he trusts and with a state apparatus that's really in financial and institutional ruin," said Edgar Gutiérrez, an analyst at San Carlos University in Guatemala.
Morales won office in a runoff Oct. 25 after the country saw months of anti-corruption demonstrations. Perez Molina and his Baldetti behind bars and facing prosecution, and the outsider's triumph was seen as a punishment vote from an electorate that wanted a fresh start.
Two and a half months later, Morales' most visible activities have included a tour of Central American nations and a visit to Guatemalan migrants' advocacy groups in the United States.
Gutiérrez said the president-elect would have been well advised to spend the last two months creating alliances to construct a government, "but he didn't do that."
Morales spokesman Heinz Heimann promised the new administration will be marked by "strict adherence to the law" and called on different sectors of civil society to play a role in leading the country, but he did not advance information on the new government's plans.
Prosecutors last week moved to lift the immunity of office for Ovalle, a lawmaker and Morales adviser. Ovalle and others are suspected of human rights abuses during the civil conflict from 1960 to 1996, in which some 245,000 people were killed or disappeared, many of them indigenous Guatemalans slain in countryside massacres.
More than a dozen retired military figures were arrested in the same case. Many of them are members of a veterans' group that supports the National Convergence Front, which Ovalle co-founded.