Nanostructured manganese oxide thin films with different crystallinity and nanomorphology were synthesized by pulsed laser deposition (PLD) in oxygen gas. Through grazing-incidence X-ray diffraction during postdeposition thermal annealing in oxidizing (air) or inert (N 2 flux) atmospheres, phase changes, crystallization onsets, and orientation effects were evaluated between room temperature and 600 °C, revealing a significant impact of growth conditions and nanoscale morphology on the X-ray patterns. Compact nanocrystalline Mn 3 O 4 films underwent first crystallization improvement between 300 and 485 °C accompanied by unit cell shrinkage, then phase transition to α-Mn 2 O 3 above 500 °C in an oxidizing environment. In contrast, during annealing under N 2 flux, crystalline Mn 3 O 4 was stable up to 600 °C, maintaining the preferential orientation promoted by PLD. Similarly, nanoporous amorphous MnO 2 films crystallized to α-Mn 2 O 3 (>480 °C) and Mn 3 O 4 (∼385 °C) in oxidizing and inert atmospheres, respectively; however, the amorphous porous morphology led to poorer crystallinity and an isotropic, powder-like crystal orientation. Quantitative analysis of structural parameters in the whole temperature range and microscopic and Raman analyses complemented the results. These findings shed light on the structural stability and nanoscale design achievable by PLD, followed by suitable annealing, of materials relevant for several technological applications.