SPC released a version for Microsoft Windows 3.0 in 1991, but its market share never approached the 70% it had previously commanded. The market leader through the late 1980s, Harvard Graphics struggled as the market shifted to Microsoft Windows. Harvard Graphics was used as bonus product with Windows 95 by Australian Retailer Harvey Norman. Version 3.0 was not released until 1991, offering improved editing functions, but its graphics and export capabilities were being outperformed by competitors like Aldus Persuasion and Lotus Freelance. Harvard Graphics 2.0 added the ability to import the latest Lotus 1-2-3 spreadsheet data before generating graphics, as well as drawing and annotations for graphs. 'Presentation' was dropped from the name for the second release, which came in 1987, developed by Mario Chaves, Carl Hu, Lenore Kirvay, and Dana Tom. Its use of vector graphics produced mixed results on the CGA and EGA displays common at the time, but output was usually sent to a slide printer or a color plotter. It could export text and graphics to Computer Graphics Metafile and to pfs:Write, also manufactured by SPC. The original version could import data from Lotus 1-2-3 or Lotus Symphony, charts created in Symphony or PFS Graph, and ASCII text.

Harvard Graphics was one of the first desktop business application software programs that allowed users to incorporate text, information graphics, and charts into custom slideshow presentations.