Focus on this lines:

res (d/transact conn [{:user/id user-id
                       :user/email email
                       :user/verification-token token}])
db-after (d/db conn)

d/transact returns a "future". The transaction is not completed yet Calling d/db immediately after d/transact, it will get a db before the transaction. To fix that:

1. Add a deref to the transaction @(d/transact ...
2. Get your db-after from the result of the transaction {:keys [db-after]} @(d/transact

Also a few tips:

• Functions that query, like check-schema, should receive a db, not a conn.
• it is possible to call (d/pull db '[*] :user/id) do pull the schema
• Please clarify if you are using datomic.client.api or datomic.api. The com.datomic/local dependency provides the datomic.client.api. The client API uses this transact syntax: (d/transact conn {:tx-data [....]})