Multi-user computer search system with methodology for bypassing instant indexing of documents. In some embodiments, for example, a system for bypassing instant indexing includes a token store storing a set of token for a current version of a document and a tokenizer server configured to tokenize a new version of the document and to generate a set of tokens for the new version of the document. The system further includes an instant indexer server configured to determine tokens to index the document by based on identified differences between the set of tokens for the new version of the document and the set of tokens for the current version of the document, to determine whether the new version of the document is a bypass document version or non-bypass document version, and to generate an index mutation for the new version of the document including a specification of whether the generated index mutation is a bypass index mutation or a non-bypass index mutation based on whether the new version of the document is a bypass document version or non-bypass document version. The system also includes an index mutation server configured to provide the generated index mutation to an index server, if the generated index mutation is a non-bypass index mutation, or not provide the generated index mutation to the index server, if the generated index mutation is a bypass index mutation.