Advanced surface engineering aims to produce surfaces with well-controlled wettabilities; however, precise control over water imbibition (WI) and liquid spreading on patterned surfaces remains a challenge. Nonthermal atmospheric plasma (NAP) treatment can dramatically change wettability; however, for coated biological objects, such as seeds, plasma interaction is not entirely understood. Herein, we employed atmospheric hybrid cold plasma to elucidate how NAP fundamentally interacts with seed surfaces. We show that NAP can control WI and liquid spreading on seeds. By investigating two distinct seed surface structures and their permeabilities, we show that the modified-surface properties are primarily due to the combined effects of enhanced physical etching and chemical functionalization. We propose the tunable surface functionalization model based on electric field-assisted electron ion-initiated impact ionization enhancing the reactive species generation. Importantly, rice seeds are not damaged by plasma treatment, and 90% of treated seeds germinate upon artificial aging. The ability to control the wettability and liquid spreading of seed surfaces can help achieve seedlings of better quality, especially in difficult-to-grow regions, including those affected by drought. Well-controlled wettability and related attributes open up new avenues for the NAP treatment of a broad range of surfaces.