CMOS Fabrication Process - Ion Implantation
As you commented, the 4e- in the valance shell of Phosphorous ion joins the bond leaving behind no free electron. But the substrate/wafer becomes positively charged because of the extra proton present in Phosphorous. So as implantation progresses, the substrate becomes more and more positive.

If we don't provide a proper method to neutralize this charge, it will get discharged either through physical contact with other materials or by arcing. This sudden discharge can damage the substrate.

In order to neutralize the charge, an apparatus is provided in which electric charge of opposite polarity (-ve) to that of the charged beam is generated near the wafer surface to neutralize the charged beam or buildup of electrostatic charge on the wafer surface (Read more ).

Coming back to the question, in ion implantation (of P), semiconductor substrate is doped with P atom not with P+ ions. The neutralization mechanism provides the extra electrons, which can move free in the wafer since all the bonds are satisfied. And that makes the wafer n-type.