Background Primary healthcare facility managers (PHFMs) occupy a unique position in the primary healthcare system, as the only cadre combining frontline clinical activities with managerial responsibilities. Often serving as ‘street-level bureaucrats,’ their perspectives can provide contextually relevant information about interventions for strengthening primary healthcare delivery, yet such perspectives are under-represented in the literature on primary healthcare strengthening. Our objective in this study was to explore perspectives of PHFMs in western Kenya regarding how to leverage human resource factors to improve immunization programs, in order to draw lessons for strengthening of primary healthcare delivery. Methods We employed a sequential mixed methods approach. We conducted in-depth interviews with key informants in Kakamega County. Emergent themes guided questionnaire development for a cross-sectional survey. We randomly selected 94 facility managers for the survey which included questions about workload, effects of workload on immunization program, and appropriate measures to address workload effects. Participants provided self-assessment of their general motivation at work, their specific motivation to ensure that all children in their catchment areas were fully immunized, and recommendations to improve motivation. Participants were asked about frequency of supervisory visits, supervisor activities during those visits, and how to improve supervision. Results The most frequently reported consequences of high workload were reduced accuracy of vaccination records (47%) and poor client counseling (47%). Hiring more clinical staff was identified as an effective remedy to high workload (69%). Few respondents (20%) felt highly motivated to ensure full immunization coverage and only 13% reported being very motivated to execute their role as a health worker generally. Increasing frequency of supervisory visits and acting on the feedback received during those visits were mostly perceived as important measures to improve program effectiveness. Conclusion Besides increasing the number of staff providing clinical care, PHFMs endorsed introducing some financial incentives contingent on specified targets and making supervisory visits meaningful with action on feedback as strategies to increase program effectiveness in primary healthcare facilities in Kenya. Targeting health worker motivation and promoting supportive supervision may reduce missed opportunities and poor client counseling in primary healthcare facilities in Kenya.