Timber frameworks are one of the most important and widespread types of structures. Their configurations and joints are usually complex and require a high level of craftsmanship to assemble. In the field of restoration, a good understanding of the structural behaviour is necessary and is often based on assessment techniques dedicated to wood characterisation. This paper presents the use of experimental modal analysis for finite element updating. To do this, several timber beams in a free supported condition were analysed in order to extract their bending natural characteristics (frequency, damping and mode shapes). Corresponding ABAQUS finite element models were derived which included the effects of local defects (holes, cracks and wood nodes), moisture and structural decay. To achieve the modal updating, additional simulations were performed in order to study the sensitivity of the mechanical parameters. With the intent to estimate their mechanical properties, a procedure of modal updating was carried out in MatLab with a Python script. This was created to extract the modal information from the ABAQUS modal analysis results to be compared with the experimental results. The updating was based on a minimum of unconstrained multivariable function using a derivative-free method. The objective function was selected from the conventional comparison tools (absolute or relative frequency difference, and/or modal assurance criterion). This testing technique was used to determine the dynamic mechanical properties of timber beams, such as the anisotropic Young's Moduli and damping ratio. To verify the modulus, a series of static 4-point bending tests and STS04 classifications were conducted. The results also revealed that local defects have a negligible influence on natural frequencies. The results demonstrate that this assessment tool offers an effective method to obtain the mechanical properties of timber elements, especially when on-site and non-destructive techniques are needed, for example when retrofitting an existing structure.