An instrument for performing microwave-assisted reactions and an associated method are disclosed. The instrument typically includes (i) a microwave-radiation source, (ii) a cavity, (iii) a waveguide in microwave communication with the microwave-radiation source and the cavity, (iv) at least one reaction-vessel sensor for determining the number and/or type of reaction vessels positioned within the cavity, (v) an interface, and (vi) a computer controller. The computer controller is typically in communication with the interface, the microwave-radiation source, and the reaction-vessel sensor. The computer controller is typically capable of determining the output of the microwave-radiation source in response to the number and/or type of reaction vessels positioned within the cavity.