Maintaining good quality of healthcare data at various levels is a critical challenge in developing countries. The barriers to healthcare data quality remain largely unexplored in eastern Ethiopia. This study aimed to assess the barriers to quality of healthcare data in urban public health facilities in the Dire Dawa city administration from 7 April to 7 May 2019. An institutional-based qualitative exploratory approach was used among 17 purposefully selected key informants. In-depth interviews were inductively coded using the ATLAS.ti 7.5.4 version software. Inductive analysis was used by semantically analyzing the explicit content of the data to determine our themes. Several key themes and subthemes with different barriers, some of which are mutually non-exclusive, were identified. These include: Organizational Barriers: Lack of an adequate health management information system and data clerk staff, poor management commitment, lack of post-training follow-up, work overload, frequent duty rotation, lack of incentives for good performers, lack of targeted feedback, and poor culture of information use. Behavioral/Individual Barriers: Gaps in the skill of managers and health professionals, lack of adequate awareness of each indicator and its definitions, inadequate educational competence, lack of feeling of ownership, poor commitment, lack of daily tallying, and lack of value for data. Technical Barriers: Lack of a standard form, diverse and too many data entry formats, manual data collection, shortage of supplies, failure to repair system break down in a timely manner, interruption in electricity and network, delay in digitizing health information systems, lack of post-training follow-up, and inadequate supervision. External Barriers: Poor collaboration between stakeholders, dependence on the software program of non-governmental organizations, and very hot weather conditions. Diverse and complex barriers to maintenance of data quality were identified. Developing standardized health management information system implementation plans, providing advanced supervisory-level training, supportive supervision, and site-level mentorship may be very effective in identifying and resolving bottleneck data quality issues. Healthcare managers should understand the imperative of data quality and accept responsibility for its improvement and maintenance. Interventions targeted only at supplies will not fully overcome limitations to data quality. Motivation of staff and recognition of best performance can motivate others and can create cooperation among staff.