diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 42beb2c44..8a5c04a00 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -644,6 +644,15 @@ describe "Config", ->
           nestedObject:
             nestedBool: true
 
+      it 'will set only the values that adhere to the schema', ->
+        expect(atom.config.set 'foo.bar',
+          anInt: 'nope'
+          nestedObject:
+            nestedBool: true
+        ).toBe true
+        expect(atom.config.get('foo.bar.anInt')).toEqual 12
+        expect(atom.config.get('foo.bar.nestedObject.nestedBool')).toEqual true
+
     describe 'when the value has an "array" type', ->
       beforeEach ->
         schema =
diff --git a/src/config.coffee b/src/config.coffee
index 14c4c817b..b82fce05e 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -404,16 +404,27 @@ Config.addSchemaValidators
     coercion: (value, schema) ->
       throw new Error('Value must be an object') if typeof value isnt 'object'
       return value unless schema.properties?
+      newValue = {}
       for prop, childSchema of schema.properties
-        value[prop] = @executeSchemaValidators(value[prop], childSchema) if prop of value
-      value
+        continue unless prop of value
+        try
+          newValue[prop] = @executeSchemaValidators(value[prop], childSchema)
+        catch error
+          ;
+      newValue
 
   'array':
     coercion: (value, schema) ->
       throw new Error('Value must be an array') unless Array.isArray(value)
       itemSchema = schema.items
       if itemSchema?
-        @executeSchemaValidators(item, itemSchema) for item in value
+        newValue = []
+        for item in value
+          try
+            newValue.push @executeSchemaValidators(item, itemSchema)
+          catch error
+            ;
+        newValue
       else
         value