I visited this museum a few weeks ago during my last few days in the Philippines.
The building is grand and beautiful, and the artwork is very neatly organized into rooms by period/influence so that you tour can be chronological (which I love).
I saw quite a few beautiful pieces, an exhibit of plant sketches that were commissioned in the early 1900s, and a beautiful contemporary mural.
There is no cafe in the museum.
I really enjoyed the visit which was not very long (approx an hour and a half), and as it is close by (walking distance) to Intramuros I would recommend doing both in the same day. Jeepneys run right on the main road that the museum is on to many places in the city.
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