Minor cracks are common types of damage in beam-like structures that must be detected early to prevent complete structural failure. Detecting and addressing such damage is crucial for maintaining structural integrity, extending service life, and minimizing operational costs. In recent years, various methods for quantifying and localizing damage using vibration measurements have been developed. However, many of these methods struggle to quantify and accurately localize the damage simultaneously. This paper addresses this challenge by applying novel hybrid multi-input and multi-output (MIMO) regression algorithms. The proposed approach combines modal analysis data, which includes frequencies, with machine learning algorithms to achieve simultaneous damage localization and quantification in damaged beams. Both numerical and experimental modal analyses have been conducted to determine the first six modal frequencies. Multiple hybrid MIMO models have been trained and tested using the frequencies obtained. The trained models have been used to estimate damage location and severity, and the results are compared. The models’ performance was evaluated using seven key metrics, including mean squared error (MSE), coefficient of determination (R2), mean absolute error (MAE), and others. The Random Forest (RF) model demonstrated exceptional performance by achieving a significantly higher R2 value of 0.997 for the precise prediction of both damage location and magnitude. Optimizing these models through hyperparameter tuning significantly improved their accuracy and reliability. This approach exhibits superior efficacy, surpassing existing models, and holds promise for advancing structural health monitoring in critical applications.