In this study, the growth mechanisms of n-type gallium nitride (GaN) cap layers for embedding nanowire-based multi-quantum-shell (NW-MQS) with a tunnel junction were investigated using the metal–organic vapor-phase epitaxy method. Herein, instead of a p-type GaN layer, n-type GaN cap layers were applied as a contact layer to the anode electrode via a tunnel junction. NW-MQSs were prepared in a rectangular grid arrangement aligning with the m- and a-axis of GaN. The growth mode of the cap layers was controlled in three stages using different growth pressures and temperatures. The first cap layer was a faceted growth mode primarily comprising the r-plane, the second was a lateral growth mode that expanded the area of the c-plane, and the third was an acceleration of lateral growth. Finally, cap layers with a flat surface were realized. Void formation in the cap layers occurred only between the NW-MQSs along the m-axis of GaN. This observation can be attributed to the difference in the coalescence of the cap layers in the a- and m-axis directions. We believe that the NW-MQS structure with the cap layer that was optimized in this study can be used as a highly efficient optical device.