Holographic optical tweezers (HOT) holds great promise for many applications in modern biophotonics, allowing the creation and measurement of minuscule forces on biomolecules, molecular motors and cells. Optical geometries used in HOT currently make use of bulk optics, and their usage in-vivo is compromised by the optically turbid nature of living tissues – a limiting factor in any advanced high-resolution imaging method. We present an alternative HOT approach in which multiple three-dimensional optical traps are introduced through a high-numerical-aperture multimode optical fibre, thus enabling an equally versatile means of optical manipulation through channels having cross-section comparable to the size of a single cell. Our work demonstrates real-time manipulation of 3-D arrangements of micro-objects, as well as the possibility of manipulating inside otherwise inaccessible cavities. We show that the position of the optical traps can be controlled with nanometric resolution over fibre lengths exceeding 100 mm. The results provide the basis for exploitation of holographic manipulation and other high-numerical-aperture techniques, including advanced forms of microscopy, through single-core-fibre endoscopes deep inside living tissues and other complex environments.