We study the stability of drum-shaped transition metal (TM)-doped boron clusters, M@Bn with n = 14 and 16, and M = 3d, 4d, and 5d TM atom using ab initio calculations. Our results show that drum-shaped M@B14 clusters are favored for M = Cr, Mn, Fe, Co, and Ni, while in other cases, open conical or bowl shaped structures become more favorable. The isoelectronic Ni@B14 and Co@B14- clusters have large highest occupied molecular orbital-lowest unoccupied molecular orbital gaps and these are magic clusters. Their stability has been correlated with the occurrence of magic behavior with 24 valence electrons in a disk jellium model, while for Fe@B14 case the drum structure is deformed and the stability occurs at 22 delocalized valence electrons. The bonding nature in these clusters has been studied by analyzing the electron density at bond and ring critical points, the Laplacian distribution of the electron density, the electron localization function, the source function, and electron localization-delocalization indices, all of which suggest two- and three-center σ bonding within and between the two B7 rings, respectively, and hybridization between the TM d orbitals and the π bonded molecular orbitals of the drum. The infrared and Raman spectra of these magic clusters show all real frequencies, suggesting the dynamical stability of the drum-shaped structures. There is a low frequency mode associated with the M atom. Results of the electronic spectra of the anion clusters are also presented that may help to identify these species in future experiments. Further, we discuss the stability of 24 delocalized valence electron systems Mn@B16 anion, Fe@B16, Co@B16 cation, and other related clusters. Assembly of Co@B14 clusters has been shown to stabilize a carbon nanotube-like nanotube of boron with Co atomic nanowire inside while a nanotube of boron with triangular network has been obtained with the assembly of Fe@B16 drum-shaped clusters. Both the nanotubes are metallic. © 2017 American Chemical Society.