We construct the crystalline comparison isomorphisms for proper smooth formal schemes over an absolutely unramified base. Such isomorphisms hold for \'etale cohomology with nontrivial coefficients, as well as in the relative setting, i.e. for proper smooth morphisms of smooth formal schemes. The proof is formulated in terms of the pro-\'etale topos introduced by Scholze, and uses his primitive comparison theorem for the structure sheaf on the pro-\'etale site. Moreover, we need to prove the Poincar\'e lemma for crystalline period sheaves, for which we adapt the idea of Andreatta and Iovita. Another ingredient for the proof is the geometric acyclicity of crystalline period sheaves, whose computation is due to Andreatta and Brinon.
Comment: Final version, to appear in Algebra and Number Theory