Judge Christopher Lopez appointed a trustee to sell Jones' assets, including his ownership stake in Free Speech Systems, the parent company of his Infowars website.
Proceeds will go to pay Jones' creditors, relatives of 20 students and six staff members killed in the 2012 mass shooting at Sandy Hook Elementary School in Newtown, Connecticut.
But Lopez declined to force Infowars itself into a separate liquidation, instead saying at a court hearing in Houston, Texas that Jones could continue to run the company until the trustee sells his ownership stake.
Lopez rejected an argument by some of the Sandy Hook families that Jones should not be allowed to regain control of his company.
The judge said the bankruptcy court's supervision had never impacted Jones' broadcasts.
"There's been lots of talk about whether Mr Jones has regained control of the business, but the reality is he never really lost it," Lopez said.
The split ruling will mean further litigation between Jones, his company, and the Sandy Hook families, including battles over $6 million in cash held by Free Speech Systems.
The families also will continue trying to collect money that Jones kept from them by sending it to his wife and father and close associates.
Lopez also resisted requests by the Sandy Hook families, who have sought control over Jones' social media accounts and the ability to choose the trustee who will be responsible for collecting assets from Jones to pay some of the $1.5 billion in defamation judgments that courts have awarded to the families.
"The thing to do is appoint an interim trustee and let that person get to work," Lopez said.
The families can vote on a permanent trustee in 30 days, and the interim trustee can weigh in on disputes in the meantime, Lopez said.
Jones filed bankruptcy protection 17 months ago, but was unable to reach a settlement that would reduce the $1.5 billion he owes to the Sandy Hook families after courts in Connecticut and Texas ruled that he defamed them with repeated false statements about the massacre.
Jones claimed for years that the Sandy Hook killings were staged with actors as part of a government plot to seize guns. He has since acknowledged that the shooting occurred.
