Scalable architectures characterized by quantum bits (qubits) with low error rates are essential to the development of a practical quantum computer. In the superconducting quantum computing implementation, understanding and minimizing materials losses is crucial to the improvement of qubit performance. A new material that has recently received particular attention is indium, a low-temperature superconductor that can be used to bond pairs of chips containing standard aluminum-based qubit circuitry. In this work, we characterize microwave loss in indium and aluminum/indium thin films on silicon substrates by measuring superconducting coplanar waveguide resonators and estimating the main loss parameters at powers down to the sub-photon regime and at temperatures between 10 and 450 mK. We compare films deposited by thermal evaporation, sputtering, and molecular beam epitaxy. We study the effects of heating in vacuum and ambient atmospheric pressure as well as the effects of pre-deposition wafer cleaning using hydrofluoric acid. The microwave measurements are supported by thin film metrology including secondary-ion mass spectrometry. For thermally evaporated and sputtered films, we find that two-level states (TLSs) are the dominating loss mechanism at low photon number and temperature. Thermally evaporated indium is determined to have a TLS loss tangent due to indium oxide of ∼ 5 × 10 −5 . The molecular beam epitaxial films show evidence of formation of a substantial indium-silicon eutectic layer, which leads to a drastic degradation in resonator performance.