The Rev. Shaun O. Harrison had a “dispute” over pot dealing with the teen he is accused of shooting on March 3 after recruiting him to sell drugs, a prosecutor said yesterday, as the fired school employee was hit with new charges from a cache of cocaine, marijuana and guns cops found in his building.

The search warrant executed March 6 on a safe in Harrison’s basement at his Roxbury home turned up: 29.5 grams of cocaine, four plastic marijuana bags, one Ruger .380, one Smith & Wesson revolver, ammo and one spent .38 shell casing, court documents said.

Harrison, 55, who has been held on $250,000 bail on an attempted murder charge, pleaded not guilty in Roxbury District Court yesterday to the additional gun and drug trafficking and possession charges. Judge Kenneth Fiandaca slapped Harrison with an additional bail of $150,000, raising his total to $400,000.

Prosecutor David Bradley said in court investigators spoke with the wounded teen — who had bullet evidence removed from his cheek — at Boston Medical Center.

Harrison is accused of shooting the 17-year-old English High School student in the back of the head as they walked alone on a Roxbury Street the night of March 3 following “a dispute over drug dealing that was going on — selling marijuana,” Bradley said.

Harrison was working as “dean of academy,” a student-parent coordinator’s job, at the Jamaica Plain school. He has been fired.

The spent shell casing found in the safe did not come from the firearm used to shoot the teen, Bradley said in court. But it was made from the same manufacturer as ammo from that gun. According to court records, Boston detectives found a .380 shell casing in a snowbank near the crime scene a few days after the shooting.

Harrison’s attorney, Michelle Brennan, called her client a “pillar of the community” and stressed he had a clean criminal record. She said, “There are a number of people who have access to that storage facility,” referring to evidence seized against Harrison.

The Rev. Vernard Coulter with the New Faith Missionary Baptist Church in Dorchester, in court yesterday, said he has known Harrison for 13 years and held a prayer service for him Monday.

Coulter said he was “shocked” by the charges against Harrison, and was praying for him and the teen.

“He’s a great guy. I love him. We continue to love him,” Coulter said about Harrison, adding, “We feel for all of them. We are not on anybody’s side, we’ll let the court and the law decide on the other stuff.”