Molybdenum oxides (MoOy) exhibit quite interesting structural, chemical, electrical, optical and electrochemical properties, which are often dependent on the synthetic procedures and fabrication conditions. The MoOy materiails are promising in numerous current and emerging technological applications, which include nanoelectronics, optoelectronics, energy storage and micromechanics. However, fundamental understanding of the crystal structure and engineering the phase and microstructure is the key to achieving the desired properties and performance in all of these applications. Therefore, in this review, an attempt made to provide a comprehensive review by considering the illustrative examples to highlight the fundamental scientific issues, challenges, and opportunities as related to various Mo-oxides applicable to electrochemical energy applications. In the course of development of lithium batteries delivering high-power and high-energy density for powering electric vehicles, here in this paper, we examine the performances of Mo-oxides, which are candidates as electrodes materials primarily for lithium-ion batteries (LIBs), while some aspects considered in sodium-ion batteries (SIBs) or electrochemical supercapacitors (ECs). Due to the wide range of oxidation states (from +6 to +2) they are promising as both positive (cathode) and negative (anode) electrodes of electrochemical cells. Based on their specific structural, chemical, electrical, and optical properties, which are dependent on the growth conditions and the fabrication technique, this review highlights the progress made in improving and understanding the electrochemical performance of MoOy compounds. Various materials (2.0 ≤ y ≤ 3.0) including anhydrous, hydrates, nanorods, nanobelts, composites and thin films of MoOy are considered. Due to their higher oxidation states, MoOy compounds undergo reversible topotactic lithium intercalation reactions; however, electrochemical features appear strongly dependent on the crystal quality and structural arrangement in the host lattice. Using in-situ and ex-situ X-ray diffraction and Raman spectroscopic data, structural characteristics of various MoOy are discussed. While the reasons for first-cycle irreversible capacity losses identified and discussed elaborately, the approaches adopted for enhanced performance and/or improvements also summarized. Several sub-stoichiometric MoOy positive electrodes exhibit excellent cycle life (up to 300 cycles) with high initial coulombic efficiency (80–90%) and large reversible capacity (>300 mAh g−1). Molybdenum oxides also categorized as one of the conversion-type transition-metal oxides and applied as negative electrodes for LIBs and SIBs with a specific capacity approaching 1000 mAh g−1. In addition to the discussion of the key aspects of crystal growth, characterization, and structure-property relationships, the future prospects to design Mo-oxide materials to enhance the structural stability and electrochemical performance are presented and discussed.