MongoDB allows for an index on a key inside of an embedded document:
db.things.ensureIndex({"address.city": 1})
Is there a way to do this using mongoengine?
class Nested(EmbeddedDocument):
    a = StringField(unique=True)
    b = StringField()
class Outer(Document):
    inner = EmbeddedDocumentField(Nested)
    c = StringField()
    meta = {"indexes": ['inner.a']}
That's all.
You can specify a field on an embedded document with unique=True:
>>> class Nested(EmbeddedDocument):
...     a = StringField(unique=True)
...     b = StringField()
... 
>>> class Outer(Document):
...     inner = EmbeddedDocumentField(Nested)
...     c = StringField()
... 
>>> o = Outer()
>>> o.c = 'abc'
>>> o.inner = Nested(a='a', b='b')
>>> o.save()
>>> o2 = Outer()
>>> o2.c = 'abc'
>>> o2.inner = Nested(a='a', b='B')
>>> o2.save()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "mongoengine/document.py", line 176, in save
    raise OperationError(message % unicode(err))
mongoengine.queryset.OperationError: Tried to save duplicate unique keys (E11000 duplicate key error index: test.outer.$inner.a_1  dup key: { : "a" })
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