Micro-manipulations of nanodiamonds (NDs) containing Nitrogen-Vacancy (NV) centers are here reviewed. Various methods such as optical tweezers, electro-kinetic trap, ions traps, optofluidics and plasmonics applied to the specific nanomaterial are reviewed, focusing on the advantages and achievements in controlling the NDs positioning for magnetic sensing. These approaches are relevant to extend magnetic sensing and imaging in different fluid environments. Levitated NDs in vacuum using optical tweezers or ions traps are also reviewed for applications in cavity optomechanics towards establishing ultra-sensitive mechanical spin hybrid systems or nano-optomechanics devices. The current demonstrations of trapped or levitated NDs containing NV centers are relevant to fundamental studies of quantum spin-photon and mechanical systems coupling but have not yet been applied directly to biological systems, as these fields of applications present several challenges.