The Stratospheric Observatory for Infrared Astronomy (SOFIA) is a 2.5m infrared telescope built into a Boeing 747 SP. In 2014 SOFIA reached its Full Operational Capability milestone and nowadays takes off about three times a week to observe the infrared sky from altitudes above most of the atmosphere’s water vapor content. An actively controlled 352mm SiC secondary mirror is used for infrared chopping with peak-to-peak amplitudes of up to 10 arcmin and chop frequencies of up to 20Hz and also as actuator for fast pointing corrections. The Swiss-made Secondary Mirror Mechanism (SMM) is a complex, highly integrated and compact flexure based mechanism that has been performing with remarkable reliability during recent years. Above mentioned capabilities are provided by the Tilt Chopper Mechanism (TCM) which is one of the two stages of the SMM. In addition the SMM is also used to establish a collimated telescope and to adjust the telescope focus depending on the structure’s temperature which ranges from about 40°C at takeoff in Palmdale, CA to about −40◦C in the stratosphere. This is achieved with the Focus Center Mechanism (FCM) which is the base stage of the SMM on which the TCM is situated. Initially the TCM was affected by strong vibrations at about 300 Hz which led to unacceptable image smearing. After some adjustments to the PID-type controller it was finally decided to develop a completely new control algorithm in state space. This pole placement controller matches the closed loop system poles to those of a Bessel filter with a corner frequency of 120 Hz for optimal square wave behavior. To reduce noise present on the position and current sensors and to estimate the velocity a static gain Kalman Filter was designed and implemented. A system inherent delay is incorporated in the Kalman filter design and measures were applied to counteract the actuators’ hysteresis. For better performance over the full operational temperature range and to represent an amplitude dependent non-linearity the underlying model of the Kalman filter adapts in real-time to those two parameters. This highly specialized controller was developed over the course of years and only the final design is introduced here. The main intention of this contribution is to present the currently achieved performance of the SOFIA chopper over the full amplitude, frequency, and temperature range. Therefore a range of data gathered during in-flight tests aboard SOFIA is displayed and explained. The SMM’s three main performance parameters are the transition time between two chop positions, the stability of the Secondary Mirror when exposed to the low pressures, low temperatures, aerodynamic, and aeroacoustic excitations present when the SOFIA observatory operates in the stratosphere at speeds of up to 850 km/h, and finally the closed-loop bandwidth available for fast pointing corrections.