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In this paper, we investigate the effects of operational conditions on structural, electronic and electrochemical properties on molybdenum suboxides (MoO3-δ) thin films. The films are prepared using pulsed-laser deposition by varying the deposition temperature (Ts), laser fluence (Φ), the partial oxygen pressure (PO2) and annealing temperature (Ta). We find that three classes of samples are obtained with different degrees of stoichiometric deviation without post-treatment: (i) amorphous MoO3-δ (δ < 0.05) (ii) nearly-stoichiometric samples (δ ≈ 0) and (iii) suboxides MoO3-δ (δ > 0.05). The suboxide films 0.05 ≤ δ ≤ 0.25 deposited on Au/Ti/SiO2/flexible-Si substrates with appropriate processing conditions show high electrochemical performance as an anode layer for lithium planar microbatteries. In the realm of simple synthesis, the MoO3-δ film deposited at 450 °C under oxygen pressure of 13 Pa is a mixture of α-MoO3 and Mo8O23 phases (15:85). The electrochemical test of the 0.15MoO3-0.85Mo8O23 film shows a specific capacity of 484 µAh cm−2 µm−1 after 100 cycles of charge-discharge at a constant current of 0.5 A cm−2 in the potential range 3.0-0.05 V.