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Best Practices for MongoDB

Here are the best practices for using MongoDB, organized into key areas: schema design, indexing, security, and query optimization. Following these practices will help you build performant, scalable, and secure...

August 28, 2025
4 minute read
By Abhijit Bhatnagar
Best Practices for MongoDB

Here are the best practices for using MongoDB, organized into key areas: schema design, indexing, security, and query optimization. Following these practices will help you build performant, scalable, and secure applications.


Schema Design: Embedding vs. Referencing

MongoDB's flexible schema is a powerful feature, but it requires careful planning. The key decision is whether to embed related data within a single document or to reference it in a separate collection.

  • Embedding is the best choice when the related data is a "has-a" relationship or is frequently accessed together. This pattern reduces the number of queries needed to fetch data, improving read performance.
    • Example: A comment document could be embedded directly within a post document, as comments are always viewed with the post.
  • Referencing is more suitable for many-to-many relationships or when the related data is large, is updated frequently, or needs to be queried independently. This pattern is similar to foreign keys in a relational database.
    • Example: In an e-commerce application, it's better to reference a user ID in an order document, as a single user can have many orders and you don't want to duplicate all user data in every order.

The golden rule is to design your schema to match your application's data access patterns. Think about how your data will be queried and updated most often.


Indexing for Performance

Indexes are crucial for fast queries. Without them, MongoDB has to perform a full collection scan, which is very inefficient.

  • Index the right fields: Create indexes on fields that you frequently use in query filters, sort operations, and join-like ($lookup) stages.
  • Use compound indexes: For queries that filter or sort on multiple fields, a compound index (an index on more than one field) is more efficient than separate single-field indexes. Remember the ESR rule for ordering fields in a compound index: Equality, Sort, Range. Put fields used for equality matches first, then those for sorting, and finally those for range queries.
  • Be mindful of cardinality: Avoid indexing fields with low cardinality (a small number of unique values), as they offer little benefit and can take up unnecessary space.
  • Use explain(): Use the db.collection.find().explain() method to analyze your query performance. It tells you which index is being used (or if a full collection scan is being performed) and provides insights into how to optimize your queries.

Query and Aggregation Optimization

Even with the right indexes, how you write your queries and aggregation pipelines can significantly impact performance.

  • Use projection: Limit the fields returned by your queries to only the ones you need. Use db.collection.find({}, { field1: 1, field2: 1 }). This reduces the amount of data transferred and processed.
  • Filter early in the pipeline: In the aggregation framework, always put the $match stage as early as possible. This filters the document set before more complex, resource-intensive stages like $group or $sort are executed.
  • Use limit() and skip() correctly: For pagination, use limit() and skip() to retrieve data in small chunks. Be aware that skip() can be slow on very large datasets, as the database still has to scan through the skipped documents.
  • Avoid large $lookup operations: While the $lookup stage allows you to join data from other collections, it can be slow on large datasets. Favor embedding for data that is frequently accessed together to avoid the need for joins.

Security Best Practices

Securing your database is non-negotiable. Don't rely on default settings.

  • Enable authentication and authorization: Always enable access control and create users with specific roles and permissions. Use the principle of least privilege, giving each user and application only the access they need.
  • Encrypt data: Use TLS/SSL to encrypt data in transit between your application and the database. For data at rest, consider a native or third-party encryption solution.
  • Limit network exposure: The database should not be accessible from the public internet. Use a firewall to restrict connections to trusted application servers and IP addresses. For cloud deployments, run your database within a private subnet of a Virtual Private Cloud (VPC).
  • Use a dedicated user account: Run the MongoDB process with a non-root, dedicated operating system user account that has minimal permissions.
  • Audit logs: Enable auditing to track all database activities, which can help you identify and respond to suspicious behavior.

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