We used a series of experiments to determine whether stable carbon isotope analysis of modern and fossil larval head capsules of chironomids allowed identification of their dietary carbon source. Our main focus was to assess whether carbon from naturally 13C-depleted methane-oxidizing bacteria (MOB) can be traced in chironomid cuticles using stable carbon isotope analysis. We first showed that a minimum sample weight of ~20 μg was required for our equipment to determine head capsule δ13C with a standard deviation of 0.5‰. Such a small minimum sample weight allows taxon-specific δ13C analyses at a precision sufficient to differentiate whether head capsules consist mainly of carbon derived from MOB or from other food sources commonly encountered in lake ecosystems. We then tested the effect of different chemical pre-treatments that are commonly used for sediment processing on δ13C measurements on head capsules. Processing with 10% KOH (2 h), 10% HCl (2 h), or 40% HF (18 h) showed no detectable effect on δ13C, whereas a combination of boiling, accelerated solvent extraction and heavy chemical oxidation resulted in a small (0.2‰) but statistically significant decrease in δ13C values. Using culturing experiments with MOB grown on 13C-labelled methane, we demonstrated that methanogenic carbon is transferred not only into the larval tissue, but also into chironomid head capsules. Taxon-specific δ13C of fossil chironomid head capsules from different lake sediments was analyzed. δ13C of head capsules generally ranged from −28 to −25.8‰, but in some instances we observed δ13C values as low as −36.9 to −31.5‰, suggesting that carbon from MOB is traceable in fossil and subfossil chironomid remains. We demonstrate that stable carbon isotope analyses of fossil chironomid head capsules can give insights into dietary links and carbon cycling in benthic food webs in the past and that the method has the potential to reconstruct the importance of MOB in the palaeo-diet of chironomid larvae and, indirectly, to infer past changes in methane flux at the sediment water interface in lakes.