The mom of accused daddy killer Thomas Gilbert Jr. is footing his legal bill.

She is also the Manhattan District Attorney’s star witness, expected to tell jurors how she came home after being sent out on an errand by her son to find her husband in a pool of blood.

And prosecutors now say that’s a glaring conflict of interest.

Gilbert, 34, shot dead his hedge-funder father in 2015, and minutes later it was his mother, Shelley Gilbert, who tragically walked in on the gruesome scene inside their Turtle Bay pad.

But Assistant District Attorney Craig Ortner raised the issue of Shelley paying the lawyer’s tab for the first time this month — even though she’s been paying the fees since his arrest.

Justice Melissa Jackson told Gilbert Tuesday in Manhattan Supreme Court that he has to waive the conflict in order to proceed to trial with his attorney, Arnold Levine.

“I want you to understand there are perceived dangers in this conflict,” Jackson cautioned Gilbert, wearing orange prison scrubs and an overgrown beard. She added that Levine will have to cross-examine his mom during the murder trial.

“What is your position on this?” she asked.

“I’m fine with the lawyer,” he replied.

But Levine said Gilbert, 34, has repeatedly refused to meet with him and asked the judge to order a mental competency exam, which she said she’d rule on later. Gilbert suffers from schizophrenia.

Shelley, who appears at every court date, has complained that her son is not getting the mental health help he needs.

He has been locked up since his arrest for killing his 70-year-old father, Thomas Gilbert Sr., Jan 5, 2015, in a dispute over his monthly allowance.

The trial date is still up in the air.