Semi-crystalline natural polymers are involved in many technological processes. Biopolymers having identical chemical compositions can differ in reactivity in heterogeneous transformations depending on their crystal structure (polymorphic modification). This paper compares the crystal structure recrystallization processes occurring in natural polysaccharides (cellulose, chitin, and starch) in the individual form and as a component of native biomass. Aqueous treatment of pre-amorphized semi-crystalline biopolymers was shown to result in swelling, thus alleviating the kinetic restrictions imposed on the restoration of crystalline regions and phase transition to the thermodynamically more stable polymorphic modification. During recrystallization, cellulose I in the individual form and within plant-based biomass undergoes a transition to the more stable cellulose II. A similar situation was demonstrated for α- and β-chitin, which recrystallize only into the α-polymorphic modification in the case of both individual polymers and native materials. Recrystallization of A-, B-, and C-type starch, both in the individual form and within plant-based flour, during aqueous treatment, results in a phase transition, predominantly to the B-type starch. The recrystallization process depends on the temperature of aqueous treatment; longer treatment duration has almost no effect on the recrystallization degree of polymers, both in the individual form and within native materials.