This paper shows the results of an experimental approach on automatic reading of 16th-century Portuguese Inquisition manuscripts using two Handwritten Text Recognition (HTR) applications. Therefore, the experiment involved modeling the handwriting of one scribe, measuring the differences between the human-made and the machine transcriptions and analyzing those differences from a palaeographic perspective. Two independently developed HTR applications were selected for the experiment: Transkribus (by ReadCoop, an European Cooperative Society) and Lapelinc Transcriptor (by LaPeLinC, Corpus Linguistic Laboratory of the State University of Southern Bahia, Brazil). Both tools use machine learning technology. The results indicated that palaeography can contribute to the development of HTR technologies in a number of ways, apart from the evident contribution of helping in the deep understanding of the results. Finally, serving both pragmatic and scientific interests. So, with this article we express the desire to promote discussions about the state-of-the-art and the challenges ahead on the road to what many already call ‘digital palaeography’ - in particular, with regard to Early Modern Portuguese manuscripts.