We demonstrate a simple, scalable approach to achieve encapsulated graphene transistors with negligible gate hysteresis, low doping levels and enhanced mobility compared to as-fabricated devices. We engineer the interface between graphene and atomic layer deposited (ALD) Al$\mathrm{<mrow\; data-mjx-texclass="ORD">2</mrow>}$O$\mathrm{<mrow\; data-mjx-texclass="ORD">3</mrow>}$ by tailoring the growth parameters to achieve effective device encapsulation whilst enabling the passivation of charge traps in the underlying gate dielectric. We relate the passivation of charge trap states in the vicinity of the graphene to conformal growth of ALD oxide governed by $in\; situ$ gaseous H$\mathrm{<mrow\; data-mjx-texclass="ORD">2</mrow>}$O pretreatments. We demonstrate the long term stability of such encapsulation techniques and the resulting insensitivity towards additional lithography steps to enable vertical device integration of graphene for multi-stacked electronics fabrication.