Novel methods are presented for the independent resonance tuning in rectangular waveguide epsilon-near-zero (ENZ) structures. This kind of tuning is achieved using short longitudinal and inclined slots placed in the middle of the ENZ channel. It is demonstrated that the tunneling frequency and Fabry–Pérot resonance (FPR) can be shifted by as much as 8% and 9.7%, respectively. Equivalent circuits for the tuning slots are given, and their equivalent parameters are extracted and validated. Analytical expressions for the equivalent slot reactances are also provided, and they show very good agreement with the extracted parameters. Experimental verification of both presented tuning methods is provided, and the agreement between simulated and experimental results is excellent (error less than 1%).