This paper investigates the application of a discrete Timoshenko beam model for estimating structural properties through model updating. It is applied to the bending modes measured on the residential tower “New Orleans” in Rotterdam. A numerical study was conducted to explore the influence of three optimization algorithms (Sequential Least Squares Quadratic Programming (SLSQP), Differential Evolution, and Particle Swarm Optimization) on the model updating. The SLSQP algorithm resulted in the most accurate parameter estimations and was therefore applied to the “New Orleans” tower. A comparison with a previous study using a uniform Euler-Bernoulli beam model indicated that the discrete Timoshenko model better matched the measured modal properties and produced structural property estimates with less variability. This is explained by the ability of the discrete beam to capture local effects more accurately. It is recommended to apply this approach on a structure where shear plays a significant role. A Bayesian framework is recommended for model updating to manage uncertainties and prevent overdetermined issues.