Context: Brown dwarfs exhibit complex atmospheric signatures, and their properties are highly sensitive to effective temperature, surface gravity, and metallicity. Several physical properties of brown dwarfs in binary systems can be well inferred from the primary, and therefore allow one to better constrain their atmospheres. Aims: We want to constrain atmospheric models of brown dwarfs in binary systems using narrow-band mid-infrared photometry. Methods: High spatial resolution and sensitivity is required to resolve the components. Therefore we have obtained deep mid-infrared images of four close binary systems with brown dwarf companions using VISIR at the Very Large Telescope (VLT) in three narrow-band filters at 8.6, 10.5 and 11.25 μm. Results: Three brown dwarf companions (GJ 229 B, HD 130948 BC and HR 7329 B) were detected at 8.6 μm. HD 130948 BC was also observed at 10.5 μm. Finally, we establish upper flux limits for the other narrow band filters with null detections. Conclusions: Our results, are in general, compatible with previous observations and model expectations for these objects. For HD 130948 BC, we conclude that there is photometric variability on a significance level of 2.8σ based on repeated observations. The bandpass around 10.5 μm appears specifically well suited for variability studies, and we speculate that either inhomogeneities in the atmospheric NH3 distribution, or silicate absorption, might cause its time-variability. Based on observations made with ESO Telescopes at the Paranal Observatories under programme IDs 076.C-0556(A) and 077.C-0438(A).