Polysilsesquioxane passivation layers were used to passivate bottom gate a-InGaZnO (a-IGZO) thin film transistors (TFT). The a-IGZO TFTs passivated with polysilsesquioxane showed highly stable behavior during positive bias stress, negative bias stress, and negative bias illumination stress. A voltage threshold shift of up to 0.1 V, less than -0.1 V and -2.3 V for positive bias stress, negative bias stress, and negative bias illumination stress, respectively. We also report the effect of reactive ion etching (RIE) on the electrical characteristics of a-InGaZnO (a-IGZO) thin-film transistors (TFT) passivated with the polysilsesquioxane-based passivation layers. We show how post-annealing treatment using two different atmosphere conditions: under O2 ambient and combination of N2 and O2 ambient (20% O2), can be performed to recover the initial characteristics. Furthermore, we present a highly stable novel polysilsesquioxane photosensitive passivation material that can be used to completely circumvent the reactive ion etching effects.