Medical Implant Embedded Controller for the Smart microPump TM and Smart nanoPump TM. The controller is based on mixed signal Application Specific Integrated Circuit (ASIC). The core is an ultra-low powered ARMs based processor with 24-bit ADC precision for flow and pressure sensors acquisition. The system boasts two individual programmable gain amplifiers (PGA) that may be driven by the two separately available current sources programmable up to 2mA each. This allows the systems to support with a variety of standard and/or custom made temperature/flow sensor based on thermocouple and RTD application. The built-in embedded controller firmware also controls the overall system power management for ultra-low power operation of up to two years of operations including the wireless telemetry that supports three different user specified operating frequencies of 125Khz, 402-405Mhz or 2.4Ghz which has a product ID of MIEC1xx, MIEC2xx or MIEC3xx, where xx indicates the bio-marker option for the Smart BioSensor TM. A value of '00' is used for controller without the Smart BioSensor TM option. The system runs a periodic background self-test based on the programmable wakeup Real-Time clock (RTC) to conserve precious battery energy and maintains system reliability.