Atom interferometers require precise control of digital, analog, and radio frequency signals for effective operation. In this paper, we propose and implement a control system for mobile atom interferometers. The system consists of a microcontroller and peripherals to synthesize radio frequency signals and to read or write analog signals. We use the system to operate a mobile atomic gravimeter by controlling 7 analog outputs, 16 digital outputs, 2 radio frequency channels, and 1 analog input. Our control system eliminates dead time between repetitions of the measurement and, consequently, improves the sampling rate of our atomic gravimeter by more than a factor of 2 and the sensitivity by more than a factor of √ 2 compared to the system based on a desktop computer.