Mid-infrared spectroscopy allows precise and label-free molecular fingerprinting of the chemical composition of bacteria. Waveguide spectroscopy promises several benefits compared to conventional ATR-FTIR spectroscopy, such as higher sensitivity and the potential for miniaturization. In this study we demonstrate mid-infrared spectroscopy of lipopolysaccharides and intact bacteria cells on a diamond waveguide with quantum cascade lasers as light source. The diamond waveguide with aluminum nitride as undercladding was tuned with a thin silicon film to specifically target the polysaccharide part of the mid-infrared spectrum (1200–1050 cm–1). It was shown to have good performance when measuring in aqueous solutions, with an order of magnitude sensitivity enhancement compared to conventional ATR-FTIR equipment. Due to the relatively low water absorptions and large differences in the absorptions of bacterial lipopolysaccharides in this spectral region, it was possible to differentiate between lipopolysaccharides obtained from different strains of Escherichia coli, as well as between Gram-positive and Gram-negative bacteria.