Aims. To understand low- to intermediate-mass star-formation in the nearby R Cr A molecular cloud, we try to identify the stellar content that is accessible with near-infrared observations. Methods. We obtained a JHKs band mosaic of ∼10 � × 60 � covering the entire R CrA molecular cloud with unprecedented sensitivity. We present a catalogue of about 3500 near-infrared sources fainter than the saturation limit Ks ∼ 10 mag, reaching Ks ∼ 18 mag. We analysed the extended sources by inspecting their morphology and point sources by means of colour–colour and colour–magnitude diagrams. Additionally, we compared the extinction inferred from the NIR data with the line-of-sight dust emission at 1.2 mm. Sources towards high dust emission but relatively low H − Ks show a projected mm-excess; these sources are either immediately surrounded by cold circumstellar material or, if too red to be a true foreground object, they are embedded in the front layer of the 1.2 mm emitting dust cloud. In both cases they are most likely associated with the cloud. Results. By means of the projected mm-excess technique we find 33 new faint near-infrared sources deeply embedded in the Coronet cluster around R CrA, for which so far about 20 bright infrared stars have been known. In contrast to the Coronet region, both the northwestern dust ridge and the southeastern cloud condensation “C” appear to be devoid of associated stars detectable with our near-infrared data. Furthermore, about a dozen sources, which are spread over the entire molecular cloud region, exhibit a possible K-band excess, but only with marginal statistical significance (<3σ), so that we do not consider the indicated K-band excess as real. Finally, while the Herbig-Haro-like objects seen on our maps are concentrated around the Coronet, we find four new nebulae also located farther down to the southeast. At the position of IRAS 18595-3712, an X-shaped bipolar nebula is resolved; its exciting star is hidden behind an edge-on disc. Conclusions. The deep near-infrared survey of the entire R CrA molecular cloud strengthens the evidence for the Coronet being the region where most of the young stars are found. Our results are consistent with earlier predictions that the R CrA cloud has fragmented into sub-condensations at different star-forming stages.