Abstract: This paper tackles the problem of jointly estimating the noise covariance matrix alongside states (parameters such as poses and points) from measurements corrupted by Gaussian noise and, if available, prior information. In such settings, the noise covariance matrix determines the weights assigned to individual measurements in the least squares problem. We show that the joint problem exhibits a convex structure and provide a full characterization of the optimal noise covariance estimate (with analytical solutions) within joint maximum a posteriori and likelihood frameworks and several variants. Leveraging this theoretical result, we propose two novel algorithms that jointly estimate the primary parameters and the noise covariance matrix. Our BCD algorithm can be easily integrated into existing nonlinear least squares solvers, with negligible per-iteration computational overhead. To validate our approach, we conduct extensive experiments across diverse scenarios and offer practical insights into their application in robotics and computer vision estimation problems with a particular focus on SLAM.