i've been back and forth on this for a project that has animators on both Blender and Maya, and the retargeting situation is still more painful than it should be in 2026. figured i'd write up what's actually causing the problems because most forum threads i found just say "check your bone orientations" without explaining the underlying issue.
The root cause is that Blender and Maya have fundamentally different bone orientation conventions. In Maya, joints point down the positive X axis by default, with Y as the up vector. Blender's armature bones point along their local Y axis (the "bone Y" direction is always bone tip minus bone root). When you export from Maya as FBX and bring the skeleton into Blender, the rig often looks fine in rest pose but the rotations are encoded differently — which means any animation baked onto that skeleton will be interpreted incorrectly on the target rig even if the visual result looks close.
what this shows up as in practice: fingers that curl the wrong direction, forearms that flip during supination, and hips that read as tilted when the character is standing straight. these are not random — they're predictable artifacts of the axis mismatch.
The workflow that's actually been working for us: we picked one canonical skeleton format (we went with a Blender-native rig using Rigify as the base) and wrote a small Maya plugin that exports joint rotations pre-transformed into Blender's bone space. the plugin is maybe 200 lines of Python and it's saved us hours per shot. on the Blender side we stopped using the built-in retarget tools and switched to Bake Action with a driver-based constraint layer — one constraint per bone that maps source rotation to target, baked out to NLA strips per shot.
the other thing nobody talks about: scale compensation at the root. if your source skeleton is 1.8m and your target is 1.75m, even a small height difference causes foot sliding that the IK constraints don't fully absorb. we ended up normalizing all source animations to a unit skeleton first, then re-scaling to target proportions using a simple ratio per bone chain.
happy to share the Maya export script if there's interest. it's not polished enough to be a proper release but it works reliably for humanoid rigs.
we hit the exact same bone orientation problem last year. ended up writing a Maya post-export script that rotates all joints to match Blender's Y-up bone convention before saving the FBX. it's ugly but it means the Blender side doesn't need any special handling. took about a day to get right and hasn't broken since.
We lost a raw take once because someone "cleaned" it directly and the cleaned version had a subtle hip artifact we didn't catch for weeks. Now raw takes are write-protected the moment they come off the suit. Extra step in the pipeline but it's saved us more than once.