<p>We study a generic cavity QED setup under conditions where the coupling between the two-level systems and a single bosonic mode is significantly degraded by low-frequency noise. To overcome this problem, we identify pulsed dynamical decoupling strategies that suppress the effects of noise while still allowing for a coherent exchange of excitations between the individual subsystems. The corresponding pulse sequences can be further designed to realize either Jaynes-Cummings, anti-Jaynes-Cummings, or Rabi couplings, as well as different types of cavity-mediated interactions between the two-level systems. A detailed analysis of the residual imperfections demonstrates that this decoupling strategy can boost the effective cooperativity of the cavity QED system by several orders of magnitude and improve the fidelity of quantum-technologically relevant operations accordingly.</p>