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- Holy Rosary Catholic (Latin rite) · Church · 139 Martin Street
- St. Benedict Church Catholic (Latin rite) · House of prayer
- Bethel United Church Church
- Church of Christ Anglican · House of prayer · 9850 Britannia Road West
- Evening Light Tabernacle House of prayer
- Grace Anglican Church Anglican · Church · 317 Main Street East
- Graceway Baptist Church Baptist · House of prayer · 103 Martin Street
- Kingdom Hall of Jehovah's Witnesses Other restorationist · House of prayer
- Knox Presbyterian Church Reformed and Presbyterian · House of prayer
- Milton Baptist Church Baptist · Church · 900 Nipissing Road
- Milton Bible Fellowship Church · 306 Ontario Street North
- New Life Church Church · 824 Thompson Road South
- Omagh Presbyterian Church Reformed and Presbyterian · Church · 8815 Britannia Road West
- Southside Community Church House of prayer · 200 Main Street East
- Southside@Main House of prayer · 200 Main Street East
- St. David's Presbyterian Church Reformed and Presbyterian · Church
- St. George's Anglican Church Anglican · Church · 7051 Guelph Line
- St. George's Lowville House of prayer
- St Paul's United Church House of prayer · 123 Main Street East