Operando synchrotron radiation-based techniques are a precious tool in battery research, as they enable the detection of metastable intermediates and ensure characterization under realistic cycling conditions. However, they do not come exempt of risks. The interaction between synchrotron radiation and samples, particularly within an active electrochemical cell, can induce relevant effects at the irradiated spot, potentially jeopardizing the experiment's reliability and biasing data interpretation. With the aim of contributing to this ongoing debate, a systematic investigation into these phenomena was carried out by conducting a root cause analysis of beam-induced effects during the operando characterization of two of the most commonly employed positive electrode materials in commercial Li-ion batteries: LiNi0.33Mn0.33Co0.33O2 and LiFePO4. The study spans across diverse experimental conditions involving different cell types and absorption and scattering techniques and seeks to correlate beam effects with factors such as radiation energy, photon flux, exposure time, and other parameters associated with radiation dosage. Finally, it provides a comprehensive set of guidelines and recommendations for assessing and mitigating beam-induced effects that may affect the outcome of battery operando experiments.