Complex reactions are difficult to control as the reactants not only produce desired product but may also further undergo unwanted reactions or the original reactants may degrade through alternate paths. This can be improved by selecting proper measurement and control. In this paper, a robust augmented derivative-free Kalman filter (augmented cubature Kalman filter, ACKF) is propounded for the continuous stirred tank reactor (CSTR) carrying out Van-de-Vusse type complex reactions where the intermediate is the desired product in the midst of consecutive and parallel reactions. Non-isothermal CSTR shows strong non-linearity with inherent challenges as the reaction kinetics depends on process temperature through Arrhenius laws and accompanies non-ideal flow behaviour and unmeasurable disturbances. First, the process exhibits inverse or non-minimum phase behaviour. Second, to control product temperature and concentration, a finite time sliding mode controller (FSMC) is suggested which effectively tracks servo response to the desired set point. Third, a disturbance filter has been proposed in association with FSMC, which constructively eliminates the input disturbances. Realistic simulations for servo-regulatory compliance, elimination of measurement noise, impact on large perturbation, and parametric uncertainty with a state-of-the-art simulator ensure the efficacy of the proposed controller. The results are analysed further with a derivative-free FSMC control approach, considering various performance indices (root mean square error (RMSE), total variation (TV), mean square deviation (MSD)) to assess the goodness of the newly developed control strategy. It has been found that improved control law (improved augmented cubature Kalman filter (IACKF)-FSMC) yields better RMSE (7.2645e–05) than ACKF-FSMC (7.5814e–05).