Metallic antiferromagnets with noncollinear orientation of magnetic moments provide a playground for investigating spin-dependent transport properties by analysis of the anomalous Hall effect. The intermetallic compound Mn5Si3 is an intinerant antiferromagnet with collinear and noncollinear magnetic structures due to Mn atoms on two inequivalent lattice sites. Here, magnetotransport measurements on polycrstalline thin films and a single crystal are reported. In all samples, an additional contribution to the anomalous Hall effect attributed to the noncollinear arrangment of magnetic moments is observed. Furthermore, an additional magnetic phase between the noncollinear and collinear regimes above a metamagnetic transition is resolved in the single crystal by the anomalous Hall effect.