PurposeTo present lessons learned from magnetic resonance imaging (MRI) quality control (QC) tests for low‐field MRI‐guided radiation therapy (MR‐IGRT) systems.MethodsMRI QC programs were established for low‐field MRI‐60Co and MRI‐Linac systems. A retrospective analysis of MRI subsystem performance covered system commissioning, operations, maintenance, and quality control. Performance issues were classified into three groups: (a) Image noise and artifact; (b) Magnetic field homogeneity and linearity; and (c) System reliability and stability.ResultsImage noise and artifacts were attributed to room noise sources, unsatisfactory system cabling, and broken RF receiver coils. Gantry angle‐dependent magnetic field inhomogeneities were more prominent on the MRI‐Linac due to the high volume of steel shielding in the gantry. B0 inhomogeneities measured in a 24‐cm spherical phantom were <5 ppm for both MR‐IGRT systems after using MRI gradient offset (MRI‐GO) compensation on the MRI‐Linac. However, significant signal dephasing occurred on the MRI‐Linac while the gantry was rotating. Spatial integrity measurements were sensitive to gradient calibration and vulnerable to shimming. The most common causes of MR‐IGRT system interruptions were software disconnects between the MRI and radiation therapy delivery subsystems caused by patient table, gantry, and multi‐leaf collimator (MLC) faults. The standard deviation (SD) of the receiver coil signal‐to‐noise ratio was 1.83 for the MRI‐60Co and 1.53 for the MRI‐Linac. The SD of the deviation from the mean for the Larmor frequency was 1.41 ppm for the MRI‐60Co and 1.54 ppm for the MRI‐Linac. The SD of the deviation from the mean for the transmitter reference amplitude was 0.90% for the MRI‐60Co and 1.68% for the MRI‐Linac. High SDs in image stability data corresponded to reports of spike noise.ConclusionsThere are significant technological challenges associated with implementing and maintaining MR‐IGRT systems. Most of the performance issues were identified and resolved during commissioning.