Treatment outcomes in patients with drug-resistant tuberculosis (DR-TB) remains unsatisfactory in the Philippines. To address this, we implemented the use of new anti-TB drugs and novel regimens. The Philippine National Tuberculosis Control Program (NTP) participated in the Bedaquiline (BDQ) Donation Program created by the US Agency for International Development and Janssen. Despite availability of donated medicine, there was a delay in the implementation of BDQ, both under operational research and programme conditions. The main challenges encountered were delayed approval by national and institutional ethics boards; limited experience of the NTP in the conduct of operational research into new drugs; and the lack of confidence of healthcare staff in the use of new and re-purposed anti-TB drugs. Technical assistance from partners and capacity building on clinical management of DR-TB and on pharmacovigilance among health workers were vital in overcoming these challenges. Over a 3-year period (from 2016-2018), 448 patients were initiated on BDQ-based regimens.