We motivate how integrated waveguides (WGs) can be part of an on-chip non-dispersive infrared sensor system for environmental sensing. We report the hurdles in maintaining WG quality when integrating emitter and detector structures on the same chip. Thus, we introduce the concept of how to determine the intrinsic loss and a process scheme to protect WG structures from damage caused during fabrication. This could pave the way to systems for environmental sensing with a minimal footprint.