Are Code Repositories Safe for Your Source Code?

Published: October 2024 | Updated: August 2026

A code repository is a centralized platform, such as GitHub, GitLab, or Bitbucket, where developers store, version, and collaborate on source code. Repositories are generally safe when properly secured, but leaked credentials, typosquatted packages, and unreviewed pull requests turn them into a common entry point for supply chain attacks.

You must have heard about source code repositories at least once in your lifetime. These repos are simply shared storage locations among developers who update them with the latest code and fixes. Organizations tend to prefer these repositories for better management and collaboration when working on software projects, which reduces the risk of losing code or using outdated versions, so it is preferred to go for version control systems like Git.

You might be wondering why you would trust another platform to securely store your code files, whether these repos are actually safe, and what to keep in mind when dealing with code repositories.

Using code repositories is an industry practice, but there have been a few cases that have made organizations more cautious when dealing with source code repository platforms. These repos have become an easy source of cyber fraud as sometimes attackers can find sensitive information in codebases like passwords, API tokens, and much more. These code repositories can also lead to supply chain attacks, causing significant financial losses, reputation damage, and business operation disruption.

However, this exposure of code repositories to cyber fraud and threats can be easily avoided using code signing procedures and some industry-trusted practices. Read on to learn about the benefits and threats these repositories possess, several cases where major players in this industry were compromised, what the consequences were, how code signing can help, and the best practices you should follow when pushing your code to a source code repository.

Introduction

A code repository, or a version control repository, is a space where developers can store and manage their source code files. It allows multiple people to work on the project and tracks each developer’s changes. Code repositories benefit organizations working on projects, especially with large teams, as they act as a centralized hub to manage and review codebase changes. However, without proper policies and security measures, these repos can become target locations for a potential cyber-attack.

You may think your code doesn’t contain any personal information that could lead to an attack and is of little importance. However, this data, when combined with active scrutiny techniques, can be leveraged to target the user for something much bigger than imagined, including credential theft, social engineering, and infrastructural attacks.

Code repositories are the best way to handle project files. They just require a safe, secure, and industry-standard approach. But before discussing best practices for using code repositories, let’s examine a few vulnerabilities that have occurred in the past when working with source code repos.

Why Shouldn’t You Blindly Trust a Code Repository?

There are many code repo platforms available, each offering diverse features and capabilities, but your codebase’s security depends on the choice you make for your repository platform. Developers across the world prefer well-known and trusted platforms such as GitHub, Bitbucket, and GitLab. Still, even some of these reliable hosts couldn’t prevent cyber-attacks in the past. In 2023, GitHub reported that an unauthorized user gained access to its systems and stole three code signing certificates.

GitHub revoked all the stolen certificates before they could be misused, but the incident illustrates the stakes: attackers could have used the certificates to sign malicious software or created fraudulent certificates that appeared legitimate, affecting customers worldwide.

Another common practice is installing packages from open-source code repositories. When a developer’s application needs a dependency, they can use packages already built by others. But sometimes attackers publish malicious code packages to infiltrate an application. In one incident, trojanized jQuery packages were pushed on npm, GitHub, and jsDelivr, leading to dependency confusion attacks, where attackers get infected code installed in place of a legitimate dependency. Around 68 infected packages were published between May 26 and June 23, 2024.

That single incident is now part of a much larger trend. Sonatype’s 2026 State of the Software Supply Chain Report identified more than 454,600 new malicious open source packages in 2025 alone, a 75% year-over-year increase (press release published January 28, 2026). You should know every detail of the code or package you’re using from a third-party platform. These repositories are an easy point of attack, and even though repository platforms provide strong security services, it is often the developer’s own choice to use unknown code that leads to a devastating incident.

Methods of Affecting a Code Repository

These attacks can take place in several ways but can also be avoided if the user pays attention to minor details and questions the authenticity of each repo. Every time a developer wants to use code available on the internet, they should ask whether other developers are actively using the repo, when it was last updated, and whether the repo was deleted at some point and later reinstated by a different maintainer.

Such basic questions can help reduce the chances of using vulnerable code in a project. Here are a few techniques attackers use to disguise their code and gain access to sensitive information.

1. Typosquatting Technique

This is one of the most popular strategies for infiltrating a system. The attacker registers a package or code repository name that closely resembles a widely used repo, only slightly altering the name. This technique has also worked on domain names; for example, attackers might tweak a domain to “www.g00gle.com” instead of “www.google.com.”

Research conducted by JFrog’s security team on PyPI, the Python Package Index, found that a “revival hijack” technique can be used to hijack roughly 22,000 current PyPI packages. This works because once a popular project’s repo is deleted from PyPI, attackers can take that repo name and publish new code under it. If a user doesn’t notice the change, they end up using infected code in their application.

By leveraging typosquatting and similar strategies, attackers take advantage of developers’ trust, which makes it crucial to verify the authenticity of any code or packages retrieved from the internet, especially those that closely resemble established names or have been reintroduced after deletion.

2. Credential Theft

One of the easiest ways to trigger a cyber-attack is if a developer commits authentication data to a code repository. This might seem like a minor, obvious thing to avoid, but it can slip a developer’s mind easily. Any credentials, tokens, or API keys committed to a repo can be used to attempt unauthorized access to that developer’s environment.

This is not a small problem. GitGuardian’s 2026 State of Secrets Sprawl report found 28.65 million new hardcoded secrets exposed on public GitHub in 2025 alone, a 34% year-over-year increase and the largest single-year jump the report has ever recorded. The exposure window matters too: the median time for an enterprise team to actually remediate a leaked secret is 94 days, according to Verizon’s 2025 Data Breach Investigations Report, a gap attackers can exploit long before anyone notices.

If you think your account doesn’t hold information an attacker could use, that’s rarely true. A stolen credential can be used to learn more about you and guess passwords for other, more important accounts, including bank profiles and social media. To help prevent this, GitHub provides repo-scanning tools like TruffleHog and Git-Secrets, which detect and block secrets before they’re committed to a repository.

3. Cloning and Modifying Repositories

While code repositories provide centralized access to everyone, public repos also let developers contribute code through pull requests. If the repo owner doesn’t properly review the code in a request before merging it, users can be blindsided when they use that repository’s code or files in their own applications.

Code review policies should include thorough processes for evaluating and approving code changes, with clear guidelines on rework and resubmission, version control practices, and documentation requirements. It was reported in early 2024 that over 100,000 GitHub repositories were infected with malicious code. Automating code analysis on pull requests with tools like SonarQube, an open-source platform that helps improve code quality, can catch many of these issues before they merge.

There are likely other techniques still undiscovered by researchers, but a basic, consistent understanding of preventive measures when deploying code to a repository goes a long way toward avoiding these attacks.

Code Repository Attack Techniques Compared

The table below summarizes the three techniques above side by side, with the primary defense for each.

Technique	How It Works	Real Incident	Primary Defense
Typosquatting / revival hijack	Registers a name nearly identical to, or recently abandoned by, a trusted package	JFrog research found ~22,000 PyPI packages vulnerable to revival hijack	Verify package names and maintainers; watch for recently revived packages
Credential / secret theft	Harvests tokens, API keys, or passwords committed to a repo	28.65 million new secrets exposed on public GitHub in 2025 alone (GitGuardian, 2026)	Secret scanning (TruffleHog, Git-Secrets); never commit credentials
Malicious pull request merges	Weak review lets tampered code get merged into a trusted repo	100,000+ GitHub repositories reported infected with malicious code in early 2024	Mandatory code review, automated analysis (e.g., SonarQube), signed commits

Best Practices

Whether simply storing files in code repositories or implementing CI/CD pipelines, everything on the web requires strong security measures and procedures. Here are some of the best practices a developer must follow to protect a code repository from being infected.

1. Code repository hosts provide security features like dependency scanning and automated vulnerability scanning. Enable these so you’re alerted when sensitive information is uploaded to the repo or an untrusted dependency is introduced.
2. Enable strong authentication methods like 2FA on all repository accounts. This adds a layer of protection even if credentials are exposed to an unauthorized user.
3. Keep up with dependency updates and regularly check your code files to maintain code integrity.
4. When working in a team on a project, limit access to the code repository to track the modifications made to it.
5. Do not store environment or config files in a code repository. Understand clearly which data is private and which can be made public.
6. Implement repository scanning tools like TruffleHog and Git-Secrets to find existing secrets and prevent future commits containing sensitive information.
7. Always enforce code signing for commits to ensure the code’s authenticity. Every repo owner should look for the cryptographic signature when a developer pushes new code, since it tells users the file was released by an authorized, credible organization.
8. Every organization or code repository owner should have an incident response plan to reduce the impact of a cyber-attack on the organization and its customers.

These practices help prevent attackers from gaining access to your code repositories. But what if you can check your code before publishing it in a repo, scan it for vulnerabilities, and confirm it isn’t already infected? Encryption Consulting’s CodeSign Secure provides all of these features, reducing the effort and time required to verify every aspect of your code.

Encryption Consulting’s CodeSign Secure

CodeSign Secure is a platform designed to digitally sign your files and attach an authentic stamp to your software. Features such as reproducible builds and pre/post hash validation, the same build-verification approach behind Encryption Consulting’s Build Verifier capability, help confirm that the code in your repository hasn’t been modified by an unknown party. CodeSign Secure integrates with CI/CD pipelines including Azure DevOps, Jenkins, GitLab, TeamCity, and Bamboo to automate code signing, which matters most on large projects with multiple contributors.

CodeSign Secure also provides vulnerability scanning, including static code analysis (SAST) and dependency scanning (SCA), which reports anomalies in your codebase, scans dependencies, and only allows a file to be signed when no vulnerabilities are found. These scans are preventive measures that give developers confidence that safe code is being pushed to a repository, helping your organization strengthen software security, build user trust, and stay aligned with industry practices and regulations.

Frequently Asked Questions

Are code repositories safe for storing source code?

Yes, when properly secured. Code repositories like GitHub, GitLab, and Bitbucket are the industry-standard way to manage source code, but leaked credentials, typosquatted dependencies, and unreviewed pull requests turn an unsecured repository into a common attack entry point.

What is typosquatting in the context of code repositories?

Typosquatting registers a package or repository name that closely resembles a popular one, hoping developers install the wrong one by mistake. Researchers at JFrog found a related “revival hijack” technique capable of affecting roughly 22,000 current PyPI packages by re-registering names abandoned by their original maintainers.

How common is credential leakage on public code repositories?

Very common and growing fast. GitGuardian’s 2026 State of Secrets Sprawl report found 28.65 million new hardcoded secrets exposed on public GitHub in 2025 alone, a 34% year-over-year increase and the largest single-year jump the report has recorded.

What is the “revival hijack” technique attackers use against package repositories?

Revival hijack exploits the gap left when a popular package is deleted from a registry like PyPI. An attacker registers the now-available name and publishes malicious code under it, and developers who don’t notice the change keep installing what they believe is the original, trusted package.

Can a malicious pull request compromise a repository even with an owner reviewing it?

Yes, if the review process is weak or rushed. Public repositories let anyone submit a pull request, and if an owner merges code without thorough review, malicious changes reach every downstream user. Reports found over 100,000 GitHub repositories infected with malicious code in early 2024 through exactly this pattern.

Does enabling 2FA actually stop repository attacks?

2FA significantly reduces account takeover risk but doesn’t stop every attack vector. Credential leaks in commit history, malicious dependencies, and unreviewed pull requests all bypass 2FA entirely, which is why it should be paired with secret scanning, dependency review, and code signing rather than relied on alone.

What happened when GitHub’s own code signing certificates were stolen in 2023?

An unauthorized party gained access to GitHub’s systems and stole three code signing certificates. GitHub revoked the stolen certificates before they were used to sign malicious software, but the incident showed that even major, security-conscious platforms aren’t immune to this kind of theft.

How does code signing protect against a compromised code repository?

Code signing lets anyone downloading code verify it came from an authorized publisher and hasn’t been altered since it left the repository. Even if a repository itself is compromised, an attacker without access to the legitimate signing key can’t make tampered code appear authentically signed.

How does CodeSign Secure help verify that repository code hasn’t been tampered with?

CodeSign Secure verifies repository code through reproducible builds and pre/post hash validation, confirming that what gets signed matches what was actually committed, and gates the signing step behind SAST and SCA vulnerability scans so known-vulnerable or anomalous code never receives a trusted signature.

Conclusion

Despite many security incidents with code repositories, they’re still considered the best-working and industry-preferred method for managing source code. Code repos are vulnerable to cyber-attacks mainly when developers don’t pay attention to what’s being uploaded and stored in them. Attackers can only take advantage when the door is left open. Follow strong security measures, perform routine code scanning, and only deploy safe, signed code, and you can avoid most theft on your source code repository.