- Ina ng Awa Parish (New Bilibid Prison)
- L'Annunziata Parish (Victoria Homes)
- Mary Cause of Joy Parish Church (Putatan)
- Mary Mother of God Parish Church (Bayanan)
- Our Lady of the Abandoned Diocesan Shrine (Poblacion)
- Our Lady of the Miraculous Medal National Shrine Parish (Sucat)
- Sacred Heart of Jesus Chaplaincy (Cupang)
- San Nicholas de Tolentino Parish Church
- San Roque Church (Alabang)
- St. James, The Great Parish (Ayala Alabang)
- St. Jerome Emiliani & Sta. Susana Parish (Ayala Alabang)
- St. Peregrine Laziosi Parish Church (Tunasan)
- Sto. Niño Chapel (Poblacion)
- Sto. Domingo Parish Church (Sucat)
- Radha Soami Satsang Beas Center Philippines
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- Alabang Church of Christ (Star Mall, Alabang)
- Alabang Full Gospel Church
- Alabang Foursquare Gospel Church (Alabang)
- Alabang New Life Christian Center (Alabang Hills Village)
- Alabang United Evangelical Church
- Bayanan IEMELIF Church
- Bible Christian Fellowship of Planas
- Cathedral of Praise - South Campus (Bellevue Hotel, Alabang)
- Christ Baptist Church (Soldiers Hills Village)
- Christ Commission Fellowship Alabang
- Christ Living Epistle Ministries Inc. (Poblacion)
- City Bible Church (Alabang)
- City Light Church (Tunasan)
- Day By Day Christian Ministries South Metro.(Starmall, Alabang)
- Divine Mercy Chapel (Poblacion)
- Door of Faith Christian Church
- Elohim Foursquare Gospel Church (Soldiers Hills Village)
- Evangelical Church of Muntinlupa (Poblacion)
- Fair Haven Baptist Church
- Faithful Jesus Church
- Greenhills Christian Fellowship South Metro
- Iglesia Ni Cristo Chapel (Putatan, Tunasan, Cupang, Sucat, Karunungan, Victoria and Alabang)
- Ina ng Awa Parish Church (NBP Reservation)
- Jesus by the Lake Worship Center (Bayanan,)
- Jesus the Living Water Christian Church (Sto. Nino Village, Tunasan)
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- Jesus the Lord of the Harvest and Victory Church (Alabang)
- Jesus, the Good Shepherd Church of Muntinlupa (National Road, Tunasan)
- Jesus Is Lord Church Muntinlupa (Putatan)
- Kordero ng Diyos Christian Church (Putatan)
- Lakeview Baptist Church (Putatan)
- Lighthouse Apostolic Ministry of Pentecost Church (Manggahan, Putatan, and New Bilibid Prison, Poblacion)
- Lighthouse Christian Community (Buencamino St., Alabang)
- Manifestation of God's Glory (Sucat)
- Muntinlupa Baptist Church (Putatan)
- Muntinlupa Christian Church (Poblacion)
- Muntinlupa Church of Christ (Poblacion)
- Muntinlupa City Foursquare Gospel Church (NBP Reservation)
- Old Line Primitive Baptist Church (Festival Supermall, Alabang)
- River of Life Christian Church (Poblacion)
- Sa Diyos Walang Imposible Ministry (Alabang)
- The True Vine Church Global Outreach Ministry] (3rd Floor DLA1 Bldg. National Road Putatan - Beside Municipal Hall )
- The Church of Jesus Christ of Latter-Day Saints (National Road, Putatan)
- The Truth Christian Ministries (Tunasan)
- Tunasan Evangelical Church
- Parkhomes United Methodist Church
- Word International Ministries Alabang (Alabang City Terminal)
- World Mission Society Church of God - Villa Carolina 1
- Villa Carolina Bible Christian Church- Villa Carolina 1 (Tunasan)
- Victory Christian Fellowship - Alabang and Muntinlupa (Tunasan)
- South City Church - Alabang Town Center
- World Mission Society Church of God
- World International Ministries (Alabang)
- South Metro Church (Primitive Baptist Church of God)(Putatan)
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