Skief has been in federal custody since Jan. 16, when he turned himself in after admitting he violated terms of his bail by continuing to steal from Harambee.
In a court filing, prosecutors said that because of the "audacious and repeated nature" of Skief's fraud, they were seeking a sentence of at least 37 months in prison instead of the 21 to 27 months they originally recommended.
U.S. District Court Judge Paul S. Diamond has told prosecutors and Skief's lawyer, Scott A. Coffina, to address the issue during sentencing.
The government said that, between the time Skief signed his plea agreement in May and pleaded guilty in August, he used a Harambee Institute debit card 43 times - including on the day he signed the plea agreement. In all, prosecutors said, he stole nearly $12,000.
Coffina has not filed a sentencing recommendation and could not be reached for comment.
Before the new theft was uncovered, Coffina had said in court documents Skief was deeply sorry for his actions. He asked the judge to sentence Skief, who had no serious criminal record, to probation with home confinement, "to enable him to continue to serve his community."
Skief - a graduate of Florida A&M University with a master's degree in education from Drexel University, who began teaching science at Harambee in 2004 - has submitted 61 letters of support, including one from John R. Stewart, the school's board president.
The West Philadelphia school, which opened in 1997, is one of the oldest charters in the state and has called itself Pennsylvania's first African-centered charter school. It is the offspring of the Harambee Institute, a community organization Skief's father, John, founded in 1972.
After John Skief died unexpectedly in December 2007 at 59, his son became CEO of both the school and the institute. Since 2006, the school has operated out of 640 N. 66th St., a building owned by the institute.
When controversy erupted in 2010 over the use of Harambee's building as a nightclub after school, the institute ended its catering services. Since then, the government found, the institute's money has come almost entirely from rent paid by the charter school.
As a result of several salary increases and at least one bonus approved by the school board, the younger Skief's base pay in 2012 was $100,000 for administering the K-8 school, which has slightly more than 500 students.
Skief has admitted stealing more than $79,000 from the Harambee Institute and taking $9,000 from a scholarship fund established in memory of his father.
To cover up the thefts, Skief presented false documents and lied to the Harambee Institute, bank officials, federal investigators, and a federal grand jury, prosecutors said.
While Skief was on bail, the judge had barred him from having access to the finances of the school or the institute.