This clinical trial focused on collating the instrumentation time and quality of root canal obturation in primary molars treated with three instrumentation techniques: adaptive, rotary, and manual. A triple-armed, randomized controlled clinical trial was performed on 75 primary molars requiring pulpectomy treatment, divided into three groups (n = 25 per group). The teeth in Group 1 were instrumented with an adaptive technique (XP-endo Shaper, FKG Dentaire, La Chaux-de-Fonds, Switzerland), Group 2 with pediatric rotary files (Kedo-S; D1 and E1), and Group 3 with a manual technique (hand K-files). The apical size of the final instrumentation was maintained at #30 for all groups. Instrumentation time and the grade of the root canal obturation were evaluated. Instrumentation duration was recorded, employing a digital stopwatch from the insertion of the first file until the completion of final irrigation. Obturation quality was assessed using radiographs. The criteria taken as a reference for obturation were: optimal (1 mm short of the apex), underfilled (2 mm short of the apex), or overfilled (beyond the apex). The use of an adaptive technique was associated with the lowest instrumentation time (p < 0.0001) when used for instrumenting primary molars and with the highest root canal filling quality of the three groups. The application of the new concept of adaptive instrumentation for pulpectomy of primary molars was a favorable technique, considering the significant reduction in instrumentation time and better obturation.