We propose an algorithm for optimizations in which the gradients contain stochastic noise. This arises, for example, in structural optimizations when computations of forces and stresses rely on methods involving Monte Carlo sampling, such as quantum Monte Carlo or neural network states, or are performed on quantum devices which have intrinsic noise. Our proposed algorithm is based on the combination of two key ingredients: an update rule derived from the steepest descent method, and a staged scheduling of the targeted statistical error and step-size, with position averaging. We compare it with commonly applied algorithms, including some of the latest machine learning optimization methods, and show that the algorithm consistently performs efficiently and robustly under realistic conditions. Applying this algorithm, we achieve a full-degree optimizations in solids using ab initio many-body computations, by auxiliary-field quantum Monte Carlo with planewaves and pseudopotentials. A new metastable structure in Si was discovered in a mixed geometry and lattice relaxing simulation. In addition to structural optimization in materials, our algorithm can potentially be useful in other problems in various fields where optimization with noisy gradients is needed.