Background: Decentralisation of health systems has been commonplace in many Low- and Middle-Income Countries (LMIC) in the last three decades. Despite several normative and theoretical arguments for decentralisation, little is known about the impact of health system reforms on vaccine systems. The contribution of vaccine systems to the reduction in childhood morbidity and mortality from vaccine-preventable diseases is significant; therefore exploring the effects of decentralisation on the vaccine systems is critical. In the 2013 policy changes in Kenya, responsibilities for vaccine systems were reconfigured. This Study explores the extent to which the quality of the vaccine systems was affected in the reconfiguration. Methods: An ethnographic approach was adopted in this qualitative Study. The researcher was partially immersed in Kilifi, Kenya, for a six-month period, obtaining an in-depth understanding of the participants’ perceptions and experiences of devolution. Thirty-eight face-to-face interviews, twenty policy-related observation events, three peer-debriefing sessions, research diaries and document reviews were used to collect and triangulate data from multiple sources. Data were exported into NVivo 12 software, coded thematically then analysed using Donabedian and Maxwell’s quality frameworks. Results: The Immunisation Programme was operationalised in a challenging context. Policy changes in the health sector were effected at lightning speed, congruent with political expectations, but in an apparent disregard of technical recommendations. The accountability mechanisms for immunisation service delivery changed from linear to a mix of linear and lateral relationships. The quality of end-to-end programmatic processes were significantly compromised, characterised by parallel procurement systems, demotivated workforce, delays in monetary outflow from Treasury to Sub-Counties. There was demonstrable commitment and heroism in the way actors absorbed the devolution shock thereby preventing the system from grinding to a halt. Conclusion: At its early stages, decentralisation had a negative impact on the quality of vaccine systems in Kenya. Executing health system decentralisation as part of a wider politically driven structural reforms can be problematic for policy planning and implementation.