The in-situ performance of heat flux plates within coarse porous substrates might be limited due to poor contact between plate and substrate. We tested this behaviour with a simple laboratory set-up. Two test substrates were placed above a reference material of known thermal conductivity between a warm and a cold plate to establish a vertical heat flux. The temperature gradients and the response of a soil heat flux plate were measured. By means of the Fourier law of heat conduction the thermal conductivity of each test substrate was calculated, thus incorporating all heat transfer within the volume and representing the ¿effective¿ conductivity. The laboratory method had an accuracy of up to ±7% (±13% for a smaller set-up). In comparison, heat flux plate-derived heat fluxes showed errors of up to 26%. Use of heat flux plates in coarse substrates is not recommended without additional measurements.