We prove the small-noise large deviation principle for the three-dimensional primitive equations with transport noise and turbulent pressure. Transport noise is important for geophysical fluid dynamics applications, as it takes into account the effect of small scales on the large scale dynamics. The main mathematical challenge is that we allow for the transport noise to act on the full horizontal velocity, therefore leading to a non-trivial turbulent pressure, which requires an involved analysis to obtain the necessary energy bounds. Both Stratonovich and Itô noise are treated.