The purpose was to investigate the surface characteristics of various resin-based materials by immersing in probiotic beverages. A total of 420 disc-shaped samples (5 mm x 2 mm) were prepared from resin-based composites. Samples were divided into four groups and immersed for 10 min/day for 1 month in either a probiotic sachet, kefir, kombucha, or artificial saliva (control). Surface roughness was measured at baseline and 1 month. One sample of each of the tested materials was examined under nanoindentation to evaluate the reduced elasticity modulus and nanohardness scores. Scanning electron microscopy (SEM) was used to compare surface differences. Data were analyzed statistically using one-way ANOVA test and the significance was set at p < .05. The lowest roughness scores were observed in Z250, Estelite Bulk Fill, and HRi ENA in most of the test groups. Among conventional composites, Z250 group had the highest nanohardness and elasticity modulus scores. Among bulk-fill composites, Estelite Bulk Fill Flow had the lowest surface roughness after immersion in probiotic beverages and the highest nanohardness values. Reveal HD, as a bulk-fill group showed higher surface roughness and considerably lower nanohardness and elasticity modulus scores. Maximum height levels of samples were recorded. SEM images revealed voids and microcracks on the surfaces of test materials. Dentists may prefer Z250 as microhybrid and Estelite Bulk Fill Flow as bulk-fill composites for the restorations of patients who consume gut-friendly drinks regularly. When there are various types of materials, nanoindentation is a useful method for evaluating surface alterations and sensible comparisons.