The influence of low-consistency refining on the surface chemical and morphological properties of softwood chemical pulp was investigated using a special laboratory refining station and advanced topochemical analyses. Refined pulp was fractionated in order to investigate the refining effect on fibres separately, without fines. The morphological properties of whole pulp and fibre fraction were studied by field-emission-SEM. X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to analyze the surface chemistry of the pulp fibres before and after refining. As a result of refining, fibre shape changed from tubular to flat. The surface coverage by extractives increased during refining together with increasing refining energy both in the whole pulp and in the fibre fraction; the increase was more significant in the whole pulp. This is probably due to leakage of hydrophobic components from the pulp fines. In the fibre fraction, surface coverage by lignin increased in the course of refining, but in the whole pulp the trend was the opposite. Similar trends were detected by observing the ToF-SIMS peaks of polysaccharides, lignin, and extractives. Refining modifies the surface chemistry and morphology of fibres, presumably by making structural changes in the fibre cell wall composition. Eventually, these changes induce increased fibre-to-fibre bonding capability and decreased scattering of light.