Security Best Practices for Custom Software
Security isn't a feature you add later — it's a property of how the software is built from day one.
Custom software gives you full control over your security posture — but that also means security is your responsibility. Unlike SaaS where the vendor handles most security concerns, custom software requires intentional security decisions at every layer.
This guide covers the essential security practices we build into every project. It's not an exhaustive security manual — it's a practical overview of what matters most for custom business applications.
Authentication Done Right
Authentication is the front door of your application. Get it wrong and everything else is irrelevant. Modern best practices include: bcrypt or Argon2 for password hashing (never MD5 or SHA-1), multi-factor authentication for sensitive operations, rate limiting on login endpoints, and account lockout after repeated failures.
For most applications, we recommend using a dedicated auth service (Auth0, Clerk, or AWS Cognito) rather than building from scratch. Authentication is too important and too complex to reinvent unless you have specific requirements that commercial services can't meet.
Strong Password Hashing
Argon2id or bcrypt with appropriate cost factors. Never store plaintext or weakly hashed passwords.
Multi-Factor Authentication
TOTP (Google Authenticator), WebAuthn (passkeys), or SMS as a fallback. MFA is non-negotiable for sensitive systems.
Rate Limiting
Limit login attempts by IP and account. Exponential backoff prevents brute force without blocking legitimate users.
Session Management
Short-lived JWTs with refresh tokens. Absolute session timeouts. Secure, httpOnly, SameSite cookies.
The OWASP Top 10 You Should Actually Worry About
The OWASP Top 10 lists the most critical web application security risks. For custom business applications, the most relevant threats are: injection attacks (SQL injection, XSS), broken access control, security misconfiguration, and vulnerable dependencies.
SQL injection is effectively eliminated by using parameterized queries or an ORM — never concatenate user input into SQL strings. XSS is mitigated by proper output encoding and Content Security Policy headers. Modern frameworks (React, Vue) handle output encoding by default, but server-rendered content and dangerouslySetInnerHTML are still common vectors.
Broken access control remains the #1 vulnerability. Always validate permissions on the server side for every request. Never rely on the frontend to enforce access rules. Implement the principle of least privilege — users should only access what they explicitly need.
Data Protection and Encryption
Encrypt data in transit (TLS 1.2+) and at rest (AES-256). This is table stakes for any modern application. All cloud providers offer encryption at rest by default for their managed databases and storage services.
For sensitive data (PII, financial information, health records), consider application-level encryption in addition to infrastructure encryption. This means data is encrypted before it's stored and decrypted only when needed, limiting exposure even if the database is compromised.
For US companies, state privacy laws like CCPA and the Washington Privacy Act require reasonable security measures proportional to the sensitivity of the data. Healthcare applications need to comply with HIPAA. Financial applications have additional requirements from the SEC and state regulators.
Secure Development Lifecycle
Security should be part of your development process, not a one-time audit. Practical steps include: dependency scanning in CI/CD (npm audit, Snyk, Dependabot), static analysis for common vulnerability patterns, code review with security-focused checklists, and regular penetration testing for production systems.
Most importantly: keep dependencies up to date. The majority of security incidents in modern applications come from known vulnerabilities in outdated packages, not sophisticated zero-day attacks. A weekly dependency update cadence dramatically reduces your attack surface.
Frequently Asked Questions
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Need Secure Custom Software?
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