Finding the true magnetic structure at given external conditions is crucial for describing magnetic materials and predicting their properties. This is especially important for high-throughput screening of potentially good magnets that without adequate description of the magnetic structure may result in enormous waste of computational resources. I introduce a method, which accurately and efficiently treats magnetic ordering in the course of standard first-principles calculations. The method is suitable for all temperatures and is based on Monte Carlo (MC) technique. At high temperatures MC is coupled to ab initio molecular dynamics, therefore treating atomic vibrations and magnetic ordering simultaneously. The method takes care of the convergence to the true ground-state magnetic structure at 0 K, coupling between spins and atomic vibrations at high temperatures, and spin-spin interactions in non-Heisenberg systems, i.e. it naturally goes beyond the usual pair-like effective exchange interactions at all temperatures. I show that the method nicely reproduces the magnetic structures at low and high temperatures even on relatively small supercells and provides a ground for truly ab initio calculations of magnetic systems in high-throughput studies. In its general formulation the MDMC method deals with non-collinear magnetism, but its collinear version may be more suitable for fast high-throughput calculations. The examples of the application of the MDMC method addressed in this paper are α-Mn; body-centered cubic Fe, which is ferromagnetic at low and paramagnetic at high temperatures; and MnB2W2, a new magnetic compound with non-trivial magnetism.