We have employed atomic force microscope-based infrared spectroscopy (AFM-IR) to spatially map energy storage polymers inside individual bacteria Rhodobacter capsulatus. AFM-IR allows chemical mapping of sub-cellular features with a spatial resolution of <100 nm. We have used key absorption bands of the energy storage polymer polyhydroxybutyrate (PHB) known from FTIR to spatially map the molecular distribution of PHB inside bacteria. We have also compared FTIR measurements on bulk PHB with AFM-IR measurements of PHB inside bacteria. We observe a shift in the location of the carbonyl absorption peak between bulk PHB and PHB inside bacteria. We have also used finite element analysis to model AFM-IR measurements of PHB granules, allowing for estimation of the real size of the granules. We have also performed transmission electron microscopy (TEM) of R. capsulatus to determine the size distribution of the PHB granules. Sizes measured by AFM-IR correspond well to TEM measurements.