We investigate Quantum Chromodynamics (QCD) in the framework of the functional renormalisation group (fRG). Thereby describing the phase transition from the phase with confined quarks into the quark-gluon-plasma phase. We focus on a physical gauge in which the mechanism driving the phase transition is discernible. We find results compatible with lattice QCD data, as well as with functional methods applied in different gauges. The phase transition is of the expected order and we computed critical exponents. Extensions of the model are discussed. When investigating the QCD phase diagram, we compute the effects of dynamical quarks at finite density on the running of the gauge coupling. Additionally, we calculate how these affect the deconfinement phase transition, also, dynamical quarks allow for the inclusion of a finite chemical potential. Concluding the investigation of the phase diagram, we establish a relation between confinement and chiral symmetry breaking, which is tied to the dynamical generation of hadron masses. In the investigations, we often encounter scale dependent fields. We will investigate a footing on which these can be dealt with in a uniform way