Many of today's Christian religious denominations have gone through highly contentious times, with multiple mergers, splits, mutinies, power battles, excommunications, shunnings, relocations, etc. Many splinter groups declared themselves to be the original pre-split group. The groups often took with them as many historical documents as possible. Lawsuits over ownership of property and documents produced court records which are also primary historical source material.
Organizational records may include payroll information, property rental and purchase documents, tax records, employment records, records of disciplinary actions, chains of command and job descriptions, etc. The records may also contain personal records (births, marriages, deaths, burials, consecrations, and ordinations.
When individuals shifted their allegiance from one group to another their church-held vital genealogical records usually were not shifted with them and remained with the parent group. The records may now be stored in the archives of the original body (which may or may not be in their original geographic location.)
If you know the dates when organizational shifts occurred or the approximate dates when your ancestors moved from one group to another, you may be abler to infer the likeliest place to begin searching for a particular record. Early public records are often spotty and incomplete or even totally lost due to floods, ,fires, or wartime rapacity. The only extant record of the marriage of your great-great-great-grandparents, who lived in California, may be housed in church archives in Florida for a group which originated in Minnesota.
Many universities and colleges with denominational ties have extensive records. Samford University (Southern Baptist) and Birmingham Southern College (Methodist) are two examples. Contact the national headquarters of your particular religious denomination and they may be able to steer you to their own historical repositories.