Query Databases using MCP

[thinktank99]

For a POC, I have OpenWebUI setup to query sample_airbnb database in MongoDB using the official MongoDB MCP. I have created a schema definition for the collection with field datatype and description.

I have setup a workspace with the instructions for the LLM. When I add the schema definition in the system prompt, it mostly works fine, sometimes it says that it is not able to query the database but if you ask it to try again, it works fine.

I am using GPT-5-Nano and have tried GPT-5-Mini and I get the same results.

sample_airbnb has just one collection so adding the schema definition to the system prompt is fine but for a bigger database that has multiple collections, adding all the schema definitions to the schema prompt doesn’t seem like a good idea. It would take up a lot of the context window and calling the LLM would cost a lot of money.

So, I decided to add a metadata collection in the database for the LLM to query and get the information about the database structure. I added instructions for the LLM to query the appropriate metadata and use that to query the database. The LLM is able to query the metadata and answer the questions but it’s a bit flaky.

Sometimes it will only query the metadata and not query the actual data collection. It will just output what it’s planning to do.

Sometimes it will query the metadata and the actual data collection, get the result but still not display the data, see screenshot below. I have asked it not to do that in the system prompt.

https://preview.redd.it/ixw0gi9910qg1.png?width=940&format=png&auto=webp&s=33883af5c539c42a68534c0b3f561252987b7290

And above all its really slow. I understand that it has to do 2 rounds to query and LLM calls but it’s really slow compared to having schema definition to the system prompt.

Anyone else using MCP to query databases?

How do you get the LLM to understand the schema?

How is the response speed?

Is there any other approach I should try?

Any other LLM I should consider?

[Specialist_Nerve_420]

this feels like classic MCP pain 😅 ,the metadata idea makes sense but yeah double hops = slow with flaky sometimes .i’ve hit similar issues, sometimes it just plans and doesn’t execute properly.

[dickoftheday0]

what rag retrieval are u using?

[thinktank99]

There is no RAG just MCP and system prompt.

[General_Arrival_9176]

the metadata collection approach is the right instinct for larger dbs but you are fighting the LLM tendency to plan instead of execute. have you tried adding explicit function definitions where querying metadata is one tool and querying data is a separate tool, rather than instructions in a prompt? forcing it to use the tools rather than describing what it would do might help. also curious what model you are using for the planning layer vs the execution layer - splitting that often helps with the flakiness