Organizations exist in order to satisfy societal needs and in the quest to fulfilling them they are faced with challenges in ever changing business environment (Johnson and Scholes, 2008). Application of strategic management system helps firms to cope with environmental changes. Strategy implementation forms the action phase of the strategic management process. It puts the formulated strategic plans into actions in order to meet the needs and expectations of their customers and achieve competitive advantage for success and survival. However, during strategy implementation there are challenges that hinder the smooth execution of the strategy plans. This study was aimed at identifying strategy implementation challenges faced by the Protestant churches in Kenya (Appendix II). The research question was answered by use of a cross-sectional study. The target population which was the units of analysis of the study was 9 Protestant Churches registered under The Registrar of Societies of Kenya. The target respondents were 3, one from the top management level and two from middle management levels of each church who where significant people to strategy implementation. The study used a questionnaire (Appendix I) to get primary data. The response rate was 96.3% i.e. 26/27 respondents from the 9 churches responded to the questionnaire. Descriptive statistics were used to analyze the collected data. The study found out that all the Protestant Churches in Kenya had vision and mission statements and had used either formal or emergent strategic plans although they rarely reviewed them. Majority of the Churches (89%) that applied formal planning practices had very clear vision statements, functional strategies, and policies in place. Most of them revealed that program strategies, functional strategies, and annual objectives are derived from corporate strategy in combination with Church Councils resolutions, management meetings, and stakeholders‟ feedback among others. Very few Churches refer to strategy plans when developing project proposals. The study established fourteen major strategy implementation challenges faced by Protestant Churches in Kenya. Among them on priority were: insufficient strategic management skills and instructions; competing activities distracting attention from implementing strategic decisions; lack of stakeholder commitment in implementing strategy; inadequate information and communication systems for monitoring the implementation process; un-supportive organizational culture; lack of sense of "ownership" of a strategy or execution xi plans among key employees; insufficient capabilities of employees involved in implementing the strategy; employees not measured or rewarded for executing the strategic plans; and insufficient financial resources to execute the strategy. Lastly the study established that the popular coping mechanism for the above challenges were: involving all stakeholders in strategy planning process; setting of clear success goals & objectives known to all employees; putting in place adequate planning, control & reporting procedures, applying organizational structural adjustment to suit the strategy, and use of mentorship or couching & teamwork spirit to implement strategy among others.