The Entrepreneurial Operating System has become one of the most widely adopted frameworks for small businesses and startups.
Founders use EOS because it creates structure.
It provides clarity.
It keeps teams aligned.
It simplifies how companies set goals, measure progress and solve issues.

But implementing EOS well requires more than worksheets and scattered documents.
Startups need software that supports the EOS rhythm with a modern, easy to use system that keeps everything in one place.

This guide breaks down the best EOS software options for startups, what features matter most and how to choose the right operating system for your team.

What EOS Software Should Actually Do

Before comparing tools, it helps to understand what EOS requires.

A true EOS friendly software should support:

Vision

• Capturing the Vision Traction Organizer
• Company values
• Target market
• Marketing strategy
• Long term goals

Traction

• Quarterly Rocks
• Weekly scorecards
• Measurables
• Weekly meetings
• Issues list
• Accountability chart
• To dos

Operating rhythm

• Quarterly planning
• Annual planning
• Weekly check ins
• Consistent accountability

If a tool cannot help you run these, it is not designed for EOS.

The Best EOS Software Options for Startups

Below are the most popular platforms that support EOS style operating rhythms. Each has strengths depending on team size, budget and desired structure.

1. Ninety.io

Ninety is the most widely used EOS software and was built specifically for companies running EOS.

Strengths

• Complete VTO builder
• Rocks, Issues, Scorecards and To Dos
• Accountability Chart
• L10 meeting agenda
• Templates for quarterly and annual planning
• Strong adoption in EOS coached companies

Ideal for

Startups that want an almost one for one software translation of EOS with minimal customization.

Limitations

• UI can feel rigid
• Not ideal if you want one system for projects, documentation or broader operations
• Does not replace your entire tech stack

2. ClickUp

ClickUp is not EOS specific, but many startups use it to organize Rocks, tasks and scorecards.

Strengths

• Extremely customizable
• Can mimic EOS workflows
• Flexible dashboards
• Good for teams needing project management and EOS in one place

Ideal for

Startups that want a project management heavy tool and are comfortable customizing their own EOS boards.

Limitations

• Can become complex fast
• Easy to drift away from EOS structure without discipline
• No built in VTO or EOS templates

3. Asana

Another tool that is not EOS specific but commonly used for Rocks and task management.

Strengths

• Simple, clean interface
• Easy task delegation
• Good for organizing quarterly Rocks into projects

Ideal for

Small teams that want a light version of EOS with simple execution workflows.

Limitations

• Lacks built in scorecards
• Lacks accountability chart
• Limited EOS rhythm support

4. Notion

A flexible tool used by many founders to create custom EOS templates.

Strengths

• Great for documentation and VTOs
• Customizable dashboards
• Easy to create meeting agendas, scorecards and Rocks templates

Ideal for

Teams wanting high flexibility and centralized knowledge.

Limitations

• Requires heavy manual setup
• No built in accountability framework
• No automated KPIs or connected operating rhythm

5. Wave

Wave is a modern Business Operating System designed to help startups achieve alignment, engagement and performance.
While not exclusively EOS software, it supports EOS tools natively while expanding into areas EOS does not cover.

Strengths

• Rocks and OKRs built in
• Scorecards with automated KPIs
• Projects, tasks and workflows
• Meetings with agendas and issue solving
• Accountability board
• Surveys, standups and weekly pulse
• Knowledge base and documentation
• CRM and KPI integrations
• Unified operating system rather than separate tools

Ideal for

Startups wanting the structure of EOS with a modern operating system that goes beyond planning and meeting rhythm.

Limitations

• More comprehensive than EOS alone, so it replaces additional parts of your stack
• Better suited for teams ready to adopt a unified system

What Startups Should Look for in EOS Software

When comparing tools, keep these criteria in mind.

Ease of Use

EOS was designed to make things simpler.
If the software adds friction, complexity or heavy training, it will not stick.

Choose a tool your team will actually use.

Built In EOS Structure

Your software should include:

• Rocks
• Scorecards
• Issues
• Accountability chart
• Meetings
• To dos
• Vision tools

Without these, you will need multiple additional tools.

Support for Weekly and Daily Rhythm

EOS only works when the cadence is consistent.
Look for tools with:

• Weekly agenda support
• Daily standups
• Progress tracking
• Accountability reminders

Ability to Grow Beyond EOS

While EOS is powerful, startups eventually need more:

• Documentation
• People management
• Surveys
• KPIs
• Projects
• CRM
• Knowledge base

Choose a system that can support your growth phases.

Should Startups Use EOS Specific Software or a Full BOS

This is the big question.

EOS specific tools (like Ninety)

• Work great for running pure EOS
• Simple and predictable
• Do not replace other tools

Business Operating Systems (like Wave)

• Support EOS but also expand beyond it
• Replace tool overload
• Bring goals, execution and team engagement into one system

Startups benefit from consolidation, especially when runway and focus are limited.

A full BOS reduces complexity, improves alignment and makes EOS easier to execute.

Final Recommendations

For most early stage startups:

• If you want pure EOS with minimal customization, choose Ninety
• If you want a customizable system you can shape, choose Notion or ClickUp
• If you want EOS plus execution, accountability, engagement and a unified operating system, choose Wave

The best EOS software is the one your team uses consistently and that reinforces your operating rhythm every day.

‍