Optical and near-infrared variability is a well-known property of young stellar objects. However, a growing number of recent studies claim that a considerable fraction of them also exhibit mid-infrared flux changes. With the aim of studying and interpreting variability on a decadal timescale, here we present a mid-infrared spectral atlas containing observations of 68 low- and intermediate-mass young stellar objects. The atlas consists of 2.5-11.6 μm low-resolution spectra obtained with the ISOPHOT-S instrument on board the Infrared Space Observatory (ISO) between 1996 and 1998, as well as 5.2-14.5 μm low-resolution spectra obtained with the Infrared Spectrograph instrument on board the Spitzer Space Telescope between 2004 and 2007. The observations were retrieved from the ISO and Spitzer archives and were post-processed interactively by our own routines. For those 47 objects where multi-epoch spectra were available, we analyze mid-infrared spectral variability on annual and/or decadal timescales. We identify 37 variable candidate sources. Many stars show wavelength-independent flux changes, possibly due to variable accretion rates. In several systems, all exhibiting 10 μm silicate emission, the variability of the 6-8 μm continuum, and the silicate feature exhibit different amplitudes. A possible explanation is variable shadowing of the silicate-emitting region by an inner disk structure of changing height or extra silicate emission from dust clouds in the disk atmosphere. Our results suggest that mid-infrared variability, in particular, the wavelength-dependent changes, is more ubiquitous than was known before. Interpreting this variability is a new possibility for exploring the structure of the disk and its dynamical processes. This work is based on observations made with the Infrared Space Observatory (ISO) and with the Spitzer Space Telescope. ISO is an ESA project with instruments funded by ESA Member States (especially the PI countries: France, Germany, the Netherlands, and UK) and with the participation of ISAS and NASA. Spitzer is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA.