High crystalline quality coaxial GaInN/GaN multiple quantum shells (MQSs) grown on dislocation-free nanowires are highly in demand for efficient white-/micro-light-emitting diodes (LEDs). Here, we propose an effective approach to improve the MQS quality during the selective growth by metal-organic chemical vapor deposition. By increasing the growth temperature of GaN barriers, the cathodoluminescent intensity yielded enhancements of 0.7 and 3.9 times in the samples with GaN and AlGaN spacers, respectively. Using an AlGaN spacer before increasing the barrier temperature, the decomposition of GaInN quantum wells was suppressed on all planes, resulting in a high internal quantum efficiency up to 69%. As revealed by scanning transmission electron microscopy (STEM) characterization, the high barrier growth temperature allowed to achieve a clear interface between GaInN quantum wells and GaN quantum barriers on the c-, r-, and m-planes of the nanowires. Moreover, the correlation between the In incorporation and structure features in MQS was quantitatively assessed based on the STEM energy-dispersive X-ray spectroscopy mapping and line-scan profiles of In and Al fractions. Ultimately, it was demonstrated that the unintentional In incorporation in GaN barriers was induced by the evaporation of predeposited In-rich particles during low-temperature growth of GaInN wells. Such residual In contamination was sufficiently inhibited by inserting low Al fraction (∼6%) AlGaN spacers after each GaInN well. During the growth of AlGaN spacers, AlN polycrystalline particles were deposited on the surrounding dummy substrate, which suppressed the evaporation of the predeposited In-rich particles. Thus, the presence of AlGaN spacers certainly improved the uniformity of In fraction through five GaInN quantum wells and reduced the diffusion of point defects from n-core to MQS active structures. The superior coaxial GaInN/GaN MQS structures with the AlGaN spacer are supposed to improve the emission efficiency in white-/micro-LEDs.