Magnetotactic bacteria provide a unique opportunity to test the applicability of statistical mechanics to living systems. Due to the presence of a unique organelle, the magnetosome, these cells possess a magnetic moment, and therefore a tendency to align with external magnetic fields. However, this alignment is never perfect because of both thermal and non-thermal noise. By performing single-cell tracking experiments, we “take the temperature” of each individual cell, that is we measure the level of noise, in two different ways: from the cells' distribution of orientations (a quantity depending only on fluctuations) and from their rotational diffusion coefficient (a quantity depending both on fluctuations and dissipation). These two independent evaluations are in agreement, and return an elevated value for the cells’ effective temperature. The rotation of flagellated bacteria is therefore greatly influenced by biological noise, and yet our results suggest that it might be described by a modified fluctuation-dissipation theorem.