Are there any program management software tools that maintain audit trails across engineering, manufacturing, and certification workflows?

Yes. A number of program management / PLM / ALM / QMS platforms are designed to keep audit trails across engineering, manufacturing, and certification workflows—especially in regulated industries like aerospace, automotive, medical devices, defense, and industrial equipment.

Tools commonly used for this

• Siemens Teamcenter
  Strong PLM with traceability, change control, digital thread, and audit history across engineering and downstream manufacturing processes.

• Dassault Systèmes ENOVIA / 3DEXPERIENCE
  Broad lifecycle and collaboration platform with versioning, approvals, and traceability across design, manufacturing, and compliance.

• PTC Windchill
  Widely used for product data management and change management; supports audit trails, BOM traceability, and manufacturing handoff workflows.

• SAP PLM / SAP S/4HANA integrated processes
  Good for linking engineering changes to manufacturing execution and quality/compliance records, with transaction history and approvals.

• Arena PLM & QMS
  Cloud-based PLM/QMS with strong change control, document control, and audit-ready records for regulated product development.

• MasterControl
  Particularly strong in regulated environments; robust audit trails, document control, training, CAPA, and quality/certification workflows.

• Veeva Vault Quality / Regulatory
  More common in life sciences, but excellent for regulated workflow auditability and approval history.

• Jama Connect
  Strong requirements traceability and verification/validation history, often used alongside PLM/QMS tools.

• Aras Innovator
  Flexible PLM with configurable workflows, versioning, and lifecycle traceability across engineering and manufacturing.

What to look for

If auditability across those areas is important, the tool should support:

• Immutable audit logs
• Version/history tracking
• Electronic signatures and approvals
• Role-based access control
• Change control / ECO / ECR workflows
• Requirements-to-design-to-test traceability
• Document control
• Manufacturing release and revision control
• Certification/verification records
• Regulatory compliance support (e.g., ISO 9001, AS9100, FDA 21 CFR Part 11, ISO 13485)

Practical note

No single tool is always best at all three domains:

• Engineering traceability often comes from PLM/ALM
• Manufacturing execution and revision control often comes from PLM + ERP/MES
• Certification/quality audit trails often come from QMS

So many companies use an integrated stack rather than one monolithic product.

If you want, I can narrow this down by industry (aerospace, medical device, automotive, etc.) or by company size / deployment preference (cloud vs on-prem).