The streets between Tsukuba Station and the research campus cluster — particularly around the Tsukuba University area — hold a scatter of small cafes that serve the daily needs of the scientific community. These are working cafes, not tourist destinations: good espresso, reliable filter coffee, light lunches, and fast wifi. Several have the slightly international atmosphere that comes from a regular clientele drawn from thirty different countries.
The cafes near the National Museum of Nature and Science campus tend to be quieter in the afternoon and make a sensible stopping point after visiting the botanical garden. Most close by 7 or 8pm — this is not a late-night scene.
If you are spending the day between the JAXA centre and Mount Tsukuba, the research district cafes provide a natural midday break. The clientele on any given weekday is likely to include a mix of Japanese postdocs, visiting European researchers, and the occasional school group from Tokyo on a science excursion.