We report calibrated microwave transmission and reflection measurements of a qubit sample holder at millikelvin temperatures. The methodology we present extends our previous work on one-port cryogenic short–open–load (SOL) calibration to a two-port SOLT measurement by implementing an unknown thru (T) standard. We report the resulting calibrated transmission and reflection at millikelvin temperatures through a printed circuit board that is installed into the sample holder. Finally, we consider a cascade of components at the end of a qubit drive line that includes (1) a cryogenic attenuator, (2) a coaxial cable, and (3) a qubit sample holder. Using experimentally determined parameters for return losses for all three components, we calculate the negligible state-preparation error in the frequency band of 5–7 GHz due to control pulse distortions arising from reflection at the coaxial launches. Taken together, our results highlight the utility of calibrated cryogenic scattering parameter measurements for the validation of qubit packaging and the wiring in its immediate vicinity.