Results. Investigating low-resolution H alpha spectra, we find that the changes in the chromosphere seem to happen mainly on a time scale longer than a few hours, but shorter variations are also observed. According to the H alpha measurements, prominences are often found in the chromosphere that reach to more than a stellar radius and are stable for weeks, and they seem to be often, but not always connected to dark photospheric spots. The rotational modulation of the H alpha emission typically seems to be anticorrelated with the light curve, but we did not find convincing evidence of a clear connection in the long-term trends of the H alpha emission and the brightness of the star. In addition, FK Com seems to be in an unusually quiet state in 2009-2010 with very little chromospheric activity and low spot contrast, which might indicate the long-term decrease in activity.