We present a micro-electro-mechanical system-based experimental technique to measure thermal conductivity of freestanding ultra-thin films of amorphous silicon nitride (Si3N4) as a function of mechanical strain. Using a combination of infrared thermal micrography and multi-physics simulation, we measured thermal conductivity of 50 nm thick silicon nitride films to observe it decrease from 2.7 W (m K)−1 at zero strain to 0.34 W (m K)−1 at about 2.4% tensile strain. We propose that such strong strain–thermal conductivity coupling is due to strain effects on fraction–phonon interaction that decreases the dominant hopping mode conduction in the amorphous silicon nitride specimens.