Moments before the execution is carried out, Joshua confronts Achan about the gravity of his actions. He declares that the impending punishment will be a precise measure-for-measure response to the catastrophe Achan brought upon the nation. Driven by deep anger, Joshua tells him that just as he polluted the people and caused a massive disaster, God will bring disaster upon him on this very day [מצודת דוד, ביאור שטיינזלץ].
Following this confrontation, a complex sequence of punishments unfolds involving both stoning and burning. One approach to understanding this dual process is that Achan was guilty of multiple offenses. The original penalty for taking the banned spoils was death by burning. However, Jericho was conquered on the Sabbath, and by stealing and carrying the spoils out, Achan violated the Sabbath, a crime punishable by stoning [רש״י, רד״ק]. Another perspective suggests Achan had committed a different severe moral sin that required stoning. To fulfill both penalties, a single heavy stone was first dropped on him, as was standard practice. Then, while he was still alive, the executioners proceeded to burn him to satisfy the penalty for violating the ban on the spoils [אלשיך]. Alternatively, some explain that the only legal sentence was burning. In this view, the initial throwing of stones was a spontaneous outburst from the enraged crowd as Achan was being led to the valley, occurring right before the formal execution by fire [רד״ק].
The varying methods of execution were directed at different targets. The burning was aimed at his inanimate property, completely destroying his tent, clothes, the stolen goods, and the rest of his belongings [רש״י, מצודת דוד, ביאור שטיינזלץ]. The subsequent stoning was directed at living creatures. Most commentators agree that his ox, donkey, and sheep were stoned [רש״י, רלב״ג, ביאור שטיינזלץ], while some add that his sons and daughters suffered this fate alongside him [מצודת דוד]. To maintain a clear boundary, the animals were stoned and burned in a completely separate process from Achan's execution, ensuring human and animal deaths were not mixed into a single event [רלב״ג].
The final act of piling stones served a dual purpose. It created a massive monument over the ashes to stand as a permanent warning for future generations. Practically, it also buried the remains deeply enough to ensure no one would ever be tempted to dig up and scavenge the melted silver and gold left behind by the fire [רלב״ג, רד״ק, אלשיך].