Current WHO guidelines recommend lifelong antiretroviral therapy (ART) for all HIV-positive individuals, including pregnant and breastfeeding women (Option B+) in settings with generalized HIV epidemics. While Option B+ is scaled-up in Kenya, insufficient adherence and retention to care could undermine the expected positive impact of Option B+. To explore challenges to the provision of Option B+ at the health facility level, we conducted forty individual gender-matched in-depth interviews with HIV-positive pregnant/postpartum women and their male partners, and four focus groups with thirty health care providers at four health facilities in western Kenya between September-November 2014. Transcripts were coded with the Dedoose software using a coding framework based on the literature, topics from interview guides, and emerging themes from transcripts. Excerpts from broad codes were then fine-coded using an inductive approach. Three major themes emerged: 1) Option B+ specific challenges (same-day initiation into treatment, health care providers unconvinced of the benefits of Option B+, insufficient training); 2) facility resource constraints (staff and drug shortages, long queues, space limitations); and 3) lack of client-friendly services (scolding of patients, inconvenient operating hours, lack of integration of services, administrative requirements). This study highlights important challenges at the health facility level related to Option B+ rollout in western Kenya. Addressing these specific challenges may increase linkage, retention and adherence to life-long ART treatment for pregnant HIV-positive women in Kenya, contribute towards elimination of mother-to-child HIV transmission, and improve maternal and child outcomes.