Miniaturization of next-generation active neural implants requires novel micro-packaging solutions that can maintain their long-term coating performance in the body. This work presents two thin-film coatings and evaluates their biostability and in vivo performance over a 7-month animal study. To evaluate the coatings on representative surfaces, two silicon microchips with different surface microtopography are used. Microchips are coated with either a ≈100 nm thick inorganic hafnium-based multilayer deposited via atomic layer deposition (ALD-ML), or a ≈6 µm thick hybrid organic–inorganic Parylene C and titanium-based ALD multilayer stack (ParC-ALD-ML). After 7 months of direct exposure to the body environment, the multilayer coatings are evaluated using optical and cross-sectional scanning electron microscopy. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is also used to evaluate the chemical stability and barrier performance of the layers after long-term exposure to body media. Results showed the excellent biostability of the 100 nm ALD-ML coating with no ionic penetration within the layer. For the ParC-ALD-ML, concurrent surface degradation and ion ingress are detected within the top ≈70 nm of the outer Parylene C layer. The results and evaluation techniques presented here can enable future material selection, packaging, and analysis, enhancing the functional stability of future chip-embedded neural implants.