The first version of the portal was developed in 2016, focusing on two aspects at that time: creating a collection of historical ciphers, alongside tools for analysing these ciphers. The content of the portal was gradually expanded, featuring a modern Angular application for browsing the database of cryptograms since 2017. The main goal was to publish accessible data for enthusiasts and researchers to support their work and to promote the research in the area of historical cryptography.

In 2019, a new education aspect was introduced, focusing on various cryptanalytic techniques. The database of cryptograms was expanded with a new separated database in 2020, and gradually upgraded in the following years. In 2021, a virtual museum and a special online tools were integrated into the portal.

The user interface of the HCPortal was redesigned in 2022. When designing new components, the contributors focused exclusively on online accessible applications and modern web technologies such as Angular, React, Laravel, etc. In the same year, a new version of the portal was introduced with a special focus on the following three aspects: education, promotion of historical cryptology, and source of historical data (databases and annotated datasets).

The education module was redesigned to better support education goals and interactive teaching methods. Old, separate databases were integrated, and access to data was updated to facilitate easier access. In 2024, an additional database of cryptologists was added as well. In 2025, a new web application was added for storing and sharing datasets used for various machine learning tasks, related to historical encrypted manuscripts and cipher keys.