Context. Most studies of the stellar and substellar populations of star-forming regions rely on using the signatures of accretion, outflows, disks, or activity characterizing the early stages of stellar evolution. However, these signatures rapidly decay with time.Aims. We present the results of a wide-area study of the stellar population of clouds in the Lupus star-forming region. When combined with 2MASS photometry, our data allow us to fit the spectral energy distributions of over 150 000 sources and identify possible new members based on their photospheric fluxes, independent of any display of the signposts of youth. Methods. We used the Wide Field Imager (WFI) at the La Silla 2.2 m telescope to image an area of more than 6 square degrees in the Lupus 1, 3 and 4 clouds in the R C , I C , and z WFI bands, selected so as to overlap with the areas observed in the Spitzer Legacy Program "From molecular cores to planet-forming disks". We complement our data with 2MASS photometry to sample the spectral energy distribution from 0.6 μm to 2.2 μm. We validate our method on the census of known members of the Lupus clouds, for which spectroscopic classification is available. The temperatures derived for cool objects are generally accurate, with most of the exceptions attributed to veiling, strong emission lines at short wavelengths, near-infrared excess, variability, or the presence of close companions. Results. Considering that the dereddened fluxes of most cool (T eff < 3500 K) young stellar objects at the distance of Lupus occupy a gap between those typical both of field cool dwarfs and of background giants, we identify a new population of cool members of Lupus 1 and 3. The approximately 130 new members are only moderately concentrated toward the densest clouds, they appear to have ages in the same range as the known members, and very few show the infrared excess caused by warm disks. This population is absent in Lupus 4. Conclusions. This new population of Lupus members seems to be composed of stars and brown dwarfs that have lost their inner disks on a timescale of a few Myr or less. Almost all these objects are in low extinction regions. We speculate that dissipation of unshielded disks caused by nearby O stars or fast collapse of the pre-(sub)stellar cores triggered by the passage of old supernova shocks may have led to disk properties and evolutionary paths very different from those resulting from the more quiescent environment provided by dense molecular clouds.