The properties of accretion disks around stars and brown dwarfs in the σ Ori cluster (age 3 Myr) are studied based on near-infrared time series photometry supported by mid-infrared spectral energy distributions. We monitor ∼ 30 young low-mass sources over 8 nights in the J-and K-band using the duPont telescope at Las Campanas. We find three objects showing variability with J-band amplitudes 0.5 mag; five additional objects exhibit low-level variations. All three highly variable sources have been previously identified as highly variable; thus we establish the long-term nature of their flux changes. The lightcurves contain periodic components with timescales of ∼ 0.5 − 8 days, but have additional irregular variations superimposed -the characteristic behaviour for classical T Tauri stars. Based on the colour variability, we conclude that hot spots are the dominant cause of the variations in two objects (#19 and #33), including one likely brown dwarf, with spot temperatures in the range of 6000-7000 K. For the third one (#2), a brown dwarf or very low mass star, inhomogenities at the inner edge of the disk are the likely origin of the variability. Based on mid-infrared data from Spitzer, we confirm that the three highly variable sources are surrounded by circum-(sub)-stellar disks. They show typical SEDs for T Tauri-like objects. Using SED models we infer an enhanced scaleheight in the disk for the object #2, which favours the detection of disk inhomogenities in lightcurves and is thus consistent with the information from variability. In the σ Ori cluster, about every fifth accreting lowmass object shows persistent high-level photometric variability. We demonstrate that estimates for fundamental parameters in such objects can be significantly improved by determining the extent and origin of the variations.