Texas Archival Resources Online " makes descriptions of the rich archival, manuscript, and museum collections in repositories across the state available to the public." You can learn more about what repositories are part of this catalog by clicking here. This website is searchable by repository or by keyword.
A search of just the word "church" brought back 1412 hits. Lots of great collections can be found including records for various Presbyterian, Pentecostal, Baptist, Lutheran, and Catholic churches as well as records for church groups like Church Women United.
If you have Texas ancestors, this is a great place to look for records.