A thorough description of the physics of a magnetic compound requires the validation of its microscopic spin Hamiltonian. Here, from the analysis of muon-spin rotation spectra recorded in the magnetically ordered state at low temperature in zero and finite magnetic fields, we determine the minimal Hamiltonian for the chiral binary intermetallic magnet MnSi, consistent with its high-temperature nonsymmorphic cubic space group P2(1)3. The model provides constraints for the orientation of the Moriya vector characterizing the microscopic Dzyaloshinskii-Moriya interaction, with respect to the Mn nearest-neighbor bonds. Small twist and canting of the magnetic structure are revealed. Our result indicates that, within experimental uncertainties, the magnetoelastic coupling is not strong enough to lower the paramagnetic crystal symmetry in the magnetically ordered state. Additional implications from our work are discussed and complementary studies are suggested.