Pit and fissure sealants play an essential role in preventive dentistry. This study evaluates the microleakage levels of a new and colored flowable composite applied as a sealant after three preparation techniques. A total of 24 non-carious mandibular permanent molars with deep pits and fissures were included in the study. Pit and fissures were prepared with 37% phosphoric acid, tungsten carbide bur and fissurotomy burs (SS WHITE Dental, New Jersey, USA) using conventional, enameloplasty and fissurotomy techniques. All samples were thermocycled following the placement of Rainbow Flow (PPH CERKAMED Wojciech Pawłowski, Poland) as a sealant and sections were taken after immersion in methylene blue dye. The microleakage levels of the samples were examined under a stereomicroscope (Olympus SZX-7 Olympus SZ-61 Stereo Microscope) at 2.8× magnification to analyze the dye penetration of the flowable composite. The 144 sections were examined and scoring for microleakage was done by examining the dye penetration from the occlusal border to the base of the fissure. Considering all sections regardless of the preparation technique, it was found that 16.6%of the sections have no leakage. Regarding the microleakage scores, the mean score of the conventional group was 1.87 ± 0.98, the mean score of the enameloplasty group was 1.88 ± 1.14, and the mean score of the fissurotomy group was 1.81 ± 1.1. The median scores of the conventional, enameloplasty and fissurotomy groups were 2, 2 and 1.5, respectively. The present study reports no difference between the microleakage level of a colored flowable composite material used as a pit and fissure sealant following three fissure preparation techniques and supports the clinical use of this material.