The disclosed technology generally relates to integrating semiconductor dies and more particularly to bonding semiconductor substrates. In an aspect, a method of bonding semiconductor substrates includes providing a first substrate and a second substrate. Each of the first substrate and the second substrate comprises a dielectric bonding layer comprising one or more a silicon carbon oxide (SiCO) layer, a silicon carbon nitride (SiCN) layer or a silicon carbide (SiC) layer. The method additionally includes, prior to bonding the first and second substrates, pre-treating each of the dielectric bonding layer of the first substrate and the dielectric bonding layer of the second substrate. Pre-treating includes a first plasma activation process in a plasma comprising an inert gas, a second plasma activation process in a plasma comprising oxygen, and a wet surface treatment including a water rinsing step or an exposure to a water-containing ambient. The method additionally includes bonding the first and the second substrates by contacting the dielectric bonding layer of the first substrate and the dielectric bonding layer of the second substrate to form a substrate assembly. The method further includes post-bond annealing the assembly.