Molybdenum oxide is an attractive material for application in several technology fields such as sensors, displays, and batteries, among many others. In this work, we present a reliable laser direct writing (LDW) method for synthesizing multi-phase molybdenum oxide (MoOx) on a single processing step. We use femtosecond laser pulses to produce up to five distinct crystalline phases of molybdenum oxide at once. We demonstrate how the laser irradiation conditions determine the MoOx stoichiometry, phase, and morphology. We show that by conveniently adjusting either the per-pulse laser fluence or the exposure time, MoOx can be obtained in nano or micro-structured form. We found that this ultrashort pulse laser processing method allows for the formation of unusual MoOx phases such as o-Mo18O52, which is rarely reported in the literature. In addition, it is possible to synthesize other sub-stoichiometric molybdenum oxide phases such as o-Mo4O11 and m-Mo8O23 all at atmospheric air conditions, with no need for demanding oxygen pressure precautions.