In lithium ion batteries, the particulate active materials (with micro- and nano-scale features) are sandwiched between metal electrodes and polymer-based separators with microscale thicknesses and infiltrated with liquid or polymer electrolytes to form operational battery cells. To achieve the desired functionality in these systems, multiples materials with varying properties must be combined together forming heterogeneous composites and the properties of the composite material depend not only on the properties of the components, but also the fabrication process (for instance, mechanical stresses during deposition that could cause alignment). This work focuses on the integration of material synthesis with thermal property measurements and physics-based analysis to provide new avenues for improved materials and device performance. In particular, high resolution infrared microscopy measures the temperature profile within “open faced” battery cells during operation, and also is used to characterize the thermal conductivity and interfaces resistances in cylindrical cell geometries with and without electrolyte. Ultimately, this work provides new insight into the thermal transport and energy generation mechanisms within lithium ion batteries useful for improving device performance and extending systems to larger form factor, higher capacity, quicker discharging cells.