The precise generation and harnessing of carbon magnetism at the single-molecule level have been captivating areas of research in chemistry and nanotechnology. However, the realization of magnetic nanographenes, also known as single-molecule π-magnets, through solution-based synthesis has proven challenging because of their high reactivity and insolubility tendency. Recent advancements in on-surface chemistry and scanning probe techniques have significantly propelled the fabrication of carbon-based magnetic nanostructures to offer a rich platform to probe quantum π-magnetism at the single-molecule level. Atomic manipulation, also referred to as probe chemistry, stands as an exciting and essential approach in the toolbox of on-surface chemistry. This approach enables site-selective chemical reactions, thereby allowing for the atomically precise imprinting and tailoring π-magnetism in a variety of nanographenes. This review highlights the recent achievements in the precise synthesis of single-molecule π-magnets using atomic manipulation. Furthermore, we also provide an outlook on the future of probe chemistry in the fabrication of this intriguing class of magnetic nanographenes, featuring designer quantum magnetism.