Embodiments herein include implantable medical devices including chemical sensors with bioerodible masking layers to allow for staged activation of the sensors. In an embodiment, an implantable medical device includes a substrate defining wells and a first chemical sensor and a second chemical sensor disposed within separate wells of the substrate. The first chemical sensor and the second chemical sensor can be configured to detect one or more analytes. The device can include a first bioerodible masking layer disposed over the second chemical sensor, sealing off the second chemical sensor. The device can further include a protective planarization layer disposed over at least one of the first chemical sensor and the second chemical sensor such that the outermost surface of the medical device over the first sensor is flush with the outermost surface of the medical device over the second sensor. Other embodiments are also included herein.