This study pursued two objectives: (1) investigating how boards in Catholic institutions navigate tensions between contractual accountability mechanisms and covenantal relationship dynamics, and (2) developing an integrated theoretical framework synthesizing organizational theory with theological traditions. The research developed the Contract-Covenant Governance Model (CCG Model) to resolve governance fragmentation in catholic and other faith-based institutions managing dual accountability to secular and religious authorities. Using qualitative thematic analysis, researchers conducted semi-structured interviews (n=28) and focus groups (n=12) with 135 participants across Catholic schools and health facilities in Uganda, representing board members, diocesan officials, and institutional staff. Analysis revealed three critical governance patterns: fragmentation where formal oversight operated separately from spiritual discernment (observed in 23 of 34 institutions studied); mission-management conflicts when regulatory requirements contradicted theological principles (25 institutions); and absence of values-based resource evaluation frameworks (29 institutions). Successful institutions integrated these elements through mission-cantered governance committees that combine technical expertise with theological reflection, and structured resource evaluation protocols assessing funding opportunities against Catholic social teaching principles. The CCG Model operationalizes five interconnected pillars—Structural Integrity (governance architecture serving mission advancement), Moral Presence (character-based leadership), Relational Representation (authentic stakeholder engagement), Mission-Aligned Resource Stewardship (values-consistent funding strategies), and Ecosystem Integration (collaborative institutional networks)—unified by Mission and Identity centrality. This framework enables simultaneous rather than sequential application of accountability mechanisms and relationshi