In transparent orthographies like German, isolated learning disabilities in either reading or spelling are common and occur as often as a combined reading and spelling disability. However, most issues surrounding the cognitive causes of these isolated or combined literacy difficulties are yet unresolved. Recently, working memory dysfunctions have been demonstrated to be promising in explaining the emergence of literacy difficulties. Thus, we applied a 2 (reading disability: yes vs. no) × 2 (spelling disability: yes vs. no) factorial design to examine distinct and overlapping working memory profiles associated with learning disabilities in reading versus spelling. Working memory was assessed in 204 third graders, and multivariate analyses of variance were conducted for each working memory component. Children with spelling disability suffered from more pronounced phonological loop impairments than those with reading disability. In contrast, domain-general central-executive dysfunctions were solely associated with reading disability, but not with spelling disability. Concerning the visuospatial sketchpad, no impairments were found. In sum, children with reading disability and those with spelling disability seem to be characterized by different working memory profiles. Thus, it is important to take both reading and spelling into account when investigating cognitive factors of literacy difficulties in transparent orthographies.