It isn't the atom that has lost an electron. It is the lattice position that is missing an electron.
The go-to example to demonstrate p-type semiconductors is silicon doped with boron. Boron has 3 electrons in its outermost orbital, and silicon has 4 electrons in its outermost orbital. Only the outermost orbital is involved in bonding. Silicon makes single covalent bonds with each of its four neighbors, when forming the silicon crystal. If you replace a silicon atom with a boron atom in this lattice, you make it such that an electron is missing from the crystal lattice, from within the energy level involved in bonding.
The substance is still net neutral, because both silicon and boron contribute a single electron for every proton they each contain. But what happens is that by introducing a trace amount of boron atoms, you create an electron vacancy that the electrons each try to fill. This vacancy is called a hole, and the holes act as if they are positive charge carriers moving through the semiconductors.