Historical manuscripts and archival documentation are handwritten texts which are the backbone sources for historical inquiry. Recent developments in the digital humanities field and the need for extracting information from the historical documents have fastened the digitization processes. Cutting edge machine learning methods are applied to extract meaning from these documents. Page segmentation (layout analysis), keyword, number and symbol spotting, handwritten text recognition algorithms are tested on historical documents. For most of the languages, these techniques are widely studied and high performance techniques are developed. However, the properties of Arabic scripts (i.e., diacritics, varying script styles, diacritics, and ligatures) create additional problems for these algorithms and, therefore, the number of research is limited. In this research, we first automatically spotted the Arabic numerals from the very first series of population registers of the Ottoman Empire conducted in the mid-nineteenth century and recognized these numbers. They are important because they held information about the number of households, registered individuals and ages of individuals. We applied a red color filter to separate numerals from the document by taking advantage of the structure of the studied registers (numerals are written in red). We first used a CNN-based segmentation method for spotting these numerals. In the second part, we annotated a local Arabic handwritten digit dataset from the spotted numerals by selecting uni-digit ones and tested the Deep Transfer Learning method from large open Arabic handwritten digit datasets for digit recognition. We achieved promising results for recognizing digits in these historical documents.