Background: In forensic ballistics, identifying ammunition types on physical evidence is critical, particularly when metallic residues are minimal. This study comparatively analyzes the elemental signatures deposited by two common projectiles—Full Metal Jacket (FMJ) (Cu/Zn jacket) and Lead Round Nose (LRN) (exposed Pb core)—on complex targets, including pig bone/tissue and mango wood. Methods: Using a semi-automatic handgun at an intermediate range of 5.0 m, residues were examined through high-resolution benchtop Micro-XRF (M4 Tornado) for micro-spatial analysis and Portable XRF (Elio) for rapid field characterization. Additionally, fresh pork leg samples were subjected to a 3-month environmental degradation period to assess trace persistence. Results: Observations indicated that LRN projectiles exhibit markedly elevated Lead (Pb) concentrations along the wound track in bone, hence confirming Pb as a reliable indicator for unjacketed ammunition; specifically, the median Pb concentrations at bullet wiping were 10.39 wt% for M4 and 7.34 wt% for Elio. Conversely, FMJ traces remain strictly confined to the surface bullet wipe area, with median concentrations of Pb, Cu, and Zn being 2.21 wt%, 0.24 wt%, and 0.59 wt% via M4, respectively. Statistical analysis showed a strong correlation for high-concentration elements on tissue, but significantly greater variance on wooden surfaces where FMJ traces exhibited a very weak negative correlation (r = −0.2774) due to minimal and irregular metal transfer. Taphonomic evaluation revealed that the Pb signature from LRN is exceptionally stable (r ≈ 0.9999) even after decomposition, while FMJ signatures are highly sensitive to environmental exposure. Conclusions: This research underscores the necessity of high-sensitivity Micro-XRF (M4) for definitive ammunition verification, providing a refined analytical framework for shooting incident reconstruction even involving degraded remains or complex environmental scenes.