The historical magnetic observatory Clementinum operated in Prague from 1839 to 1926. The data from the yearbooks that recorded the observations at Clementinum have recently been digitized and were subsequently converted, in this work, into the physical units of the International System of Units (SI). Introducing a database of geomagnetic data from this historical source is a part of our paper. Some controversial data are also analysed here. In the original historical sources, we identified an error in using the physical units. It was probably introduced by the observers determining the temperature coefficient of the bifilar apparatus. By recalculating the values in the records, some missing values are added; for instance, the temperature coefficients for the bifilar magnetometer, the baselines, and the annual averages for the horizontal intensity in the first years of observations were redetermined. The values of absolute measurements of the declination in 1852, which could not be found in the original sources, were also estimated. The main contribution of this article rests in critically reviewed information about the magnetic observations in Prague, which is, so far, more complete than any other. The work also contributes to the space weather topic by revealing a record of the now almost forgotten magnetic disturbance of 3 September 1839.