Careful cleaning and disinfection of pigpens is essential to prevent disease spread and avoid the resultant economic losses. Hygiene in pigpens is generally evaluated by visual monitoring supplemented with bacteriological monitoring, which includes counting the total aerobic bacteria (TAB) and/or fecal indicator bacteria (FIB). However, these methods present drawbacks such as time and labor requirements. As adenosine triphosphate (ATP) is ubiquitous in all living organisms including microorganisms, this study aimed to directly compare the results of microbial assessment and ATP quantification, and to suggest possible detailed application methods of the ATP test for hygiene evaluation in pigpens of a farrowing unit. Before and after standard cleaning procedures, samples were collected from the floor corner, floor center, and feeding trough of four pigpens at different time points. No FIB were detected and both the TAB and ATP levels were significantly decreased in the floor center area after cleaning. FIB were continuously detected after cleaning and disinfection of the floor corners, and there was no significant ATP level reduction. The feeding trough did not show any significant difference in these values before and after cleaning, indicating insufficient cleaning of this area. The levels of TAB and ATP after cleaning were significantly correlated and the average ATP value was significantly lower in the absence of FIB than in their presence. In the absence of standard references, a more thorough hygiene management could be achieved evenly by supplementing cleaning or disinfection based on the lowest ATP results obtained at the cleanest test site, which in the present study was the floor center. Overall, these results indicate that the on-farm ATP test can be used to determine the cleanliness status, in addition to visual inspection, as an alternative to laboratory culture-based testing for the presence of microorganisms.