What to Do When Your Building Permit Gets Denied

The Letter Nobody Wants to Receive

You have invested thousands of dollars in architectural plans, weeks of design decisions, and months of anticipation. Then you receive notice from the building department: your permit application has been denied.

A permit denial feels like a wall. But in most cases, it is more like a detour. The vast majority of denied permits in Bay Area jurisdictions are eventually approved after plan revisions, additional documentation, or minor design modifications. Understanding why your permit was denied and what to do next is the difference between a manageable delay and a project-ending roadblock.

Building codes and permit requirements change. Verify current requirements with your local building department before starting any project.

Common Reasons Building Permits Get Denied

Every building department reviews permit applications against two primary frameworks: the California Building Code (CBC) and local zoning ordinances. Denials almost always trace back to a conflict with one or both.

Incomplete Application or Missing Documents

This is the most common reason for denial, and also the easiest to fix. Building departments require a specific set of documents that varies by project type and jurisdiction. Common missing items include:

• Structural calculations signed by a licensed engineer
• Title 24 energy compliance reports
• Site plans showing property lines, setbacks, and easements
• Detailed construction drawings with proper dimensions and specifications
• Soils reports (for foundation work or hillside properties)
• Historical review documentation (for designated or potential historic structures)

An incomplete application is typically returned with a checklist of required items rather than a formal denial. Providing the missing documents resolves the issue.

Zoning Violations

Zoning regulations control what can be built on a given property: how large, how tall, how far from property lines, and sometimes what it can be used for. Common zoning conflicts include:

• Setback violations. Your addition or new structure encroaches on the required distance from a property line, street, or neighboring building.
• Lot coverage. The total building footprint exceeds the maximum percentage of the lot allowed to be covered by structures.
• Height limits. Your project exceeds the maximum building height for your zoning district.
• Floor area ratio (FAR). The total floor area of all structures on the lot exceeds the allowed ratio to lot size.
• Use restrictions. The proposed use (such as an ADU, home office, or commercial activity) is not permitted in the zoning district.

Structural or Engineering Concerns

The building department may reject plans that do not demonstrate adequate structural integrity. This is especially common for:

• Second-story additions where the existing foundation has not been evaluated
• Removal of load-bearing walls without proper beam and post specifications
• Hillside construction without adequate soils and geotechnical reports
• Seismic retrofit work that does not meet current standards

Neighborhood or Historic Preservation Conflicts

In some Bay Area communities, particularly older neighborhoods in San Francisco, Palo Alto, and other Peninsula cities, projects must pass design review or comply with historic preservation guidelines. A project that meets all code requirements may still be denied if it conflicts with neighborhood character standards, historic district guidelines, or protected sight lines.

Previous Unpermitted Work

If the building department discovers unpermitted work on your property during the review process, they may deny the new permit until the existing violations are resolved. This is a common issue in Bay Area homes where previous owners made modifications without permits.

What to Do: Step by Step

Step 1: Get the Denial in Writing

Request a detailed written explanation of the denial, including the specific code sections or zoning ordinances your project violates. A verbal explanation from the plan checker is helpful, but you need the written record to guide your revisions.

Step 2: Understand the Specific Objections

Read the denial carefully and identify whether the issues are:

• Administrative (missing documents, incomplete forms): These are simple to resolve.
• Code-related (structural deficiencies, energy compliance, accessibility): These require plan revisions by your architect or engineer.
• Zoning-related (setbacks, height, FAR, lot coverage): These may require design changes or a variance application.
• Discretionary (design review, historic preservation): These may require a hearing or appeal.

Step 3: Schedule a Meeting with the Plan Checker

Most Bay Area building departments allow applicants to schedule a meeting with the plan checker who reviewed the application. This meeting is invaluable. You can ask specific questions about what changes would satisfy the objections, what documentation is needed, and whether there are alternative approaches the department would accept.

Come prepared with your plans, the denial letter, and specific questions. Building department staff are generally willing to help applicants find a path to approval.

Step 4: Revise and Resubmit

Work with your architect, engineer, or design-build firm to revise the plans addressing each cited objection. Common revisions include:

• Adding missing structural calculations or energy reports
• Adjusting setbacks by reducing the building footprint
• Lowering the roof height or changing the roof pitch
• Modifying the design to comply with historic district guidelines
• Correcting dimensioning and specification errors

Submit the revised plans with a cover letter that specifically addresses each point in the denial. This helps the plan checker see that every objection has been resolved.

Step 5: Consider a Variance (If Needed)

If your project cannot meet a zoning requirement through design revision, you may be able to apply for a variance. A variance is a legal exception to a specific zoning regulation. The process typically involves:

1. Filing a variance application with supporting documentation
2. Posting public notice on your property
3. Notifying neighbors within a specified radius (usually 300-500 feet)
4. Attending a hearing before the planning commission or zoning board
5. Presenting evidence of hardship unique to your property

Variances are not guaranteed. The applicant must typically demonstrate that strict application of the zoning rule creates an undue hardship related to the physical characteristics of the property (such as an unusual shape, slope, or size) rather than personal preference or financial considerations.

Step 6: Appeal (If Appropriate)

If you believe the denial was based on an incorrect interpretation of the code, you have the right to appeal. The appeal process varies by jurisdiction but generally involves:

• Filing an appeal within 10-30 days of the denial
• Paying an appeal fee (typically $300-$1,500)
• Preparing a written argument explaining why the denial was incorrect
• Presenting your case at an appeals board hearing

Appeals are most effective when you have a clear code interpretation issue, not simply a disagreement with the regulations themselves.

The Cost of Permit Delays

A denied permit does not just delay construction. It creates cascading costs.

Delay Impact	Typical Cost
Architect/engineer plan revisions	$1,000 - $5,000+
Variance application and hearing	$1,500 - $5,000
Extended timeline (holding contractor, material storage)	$2,000 - $10,000/month
Resubmission fees	$200 - $2,000
Extended temporary housing (if displaced)	$3,000 - $10,000/month

For a major remodel or addition, a 2-3 month permit delay can add $10,000-$30,000 or more to the total project cost when all factors are considered.

How to Prevent Permit Denials

Research Zoning Before You Design

Before investing in architectural plans, research your property’s zoning designation, setback requirements, height limits, FAR limits, and lot coverage maximums. This information is typically available from your city’s planning department website or at the counter. Designing within known constraints from the start eliminates the most common causes of denial.

Hire Professionals Who Know Your Jurisdiction

Every Bay Area building department has its own culture, priorities, and interpretation tendencies. An architect or design-build firm that has successfully permitted multiple projects in your city understands what the plan checkers look for, what level of detail they expect, and what design approaches tend to trigger objections.

Submit Complete Applications

Incomplete applications are the most common reason for rejection. Before submitting, verify that you have every required document, form, and report. Many building departments publish checklists on their websites. Use them.

Address Neighbor Concerns Proactively

For projects that require design review or variance hearings, neighbor support or opposition can influence the outcome. Talk to your neighbors before you submit. Explain the project, listen to their concerns, and make reasonable accommodations. A letter of support from an adjacent neighbor carries significant weight at a hearing.

How Design-Build Firms Handle Permitting

At Custom Home Design and Build, permitting is built into our process rather than treated as an afterthought. Our approach includes:

• Zoning analysis during feasibility. Before we begin design, we research your property’s zoning constraints and identify any potential conflicts early.
• Code-compliant design from the start. Our design team works within known code and zoning requirements, so the plans are buildable and permittable from day one.
• Complete submission packages. We prepare and submit permit applications with all required documents, calculations, and reports. Incomplete applications waste time and money.
• Relationship with local departments. Our team has permitted projects across Bay Area jurisdictions and understands the specific requirements and review processes of each.
• Plan check coordination. When plan check comments are received, we address them promptly and resubmit with detailed responses.

This proactive approach means that permit denials are rare for our projects, and when plan check comments do arise, they are resolved quickly.

Move Forward with Confidence

A permit denial is a setback, not a dead end. By understanding the specific reasons, working with experienced professionals, and addressing each objection methodically, you can get your project approved and back on track.

If you want to avoid permit headaches from the start, working with a design-build firm that handles permitting as part of the process is your strongest option.

Contact Custom Home Design and Build to learn how we guide Bay Area homeowners through the permitting process, from initial zoning research to final permit approval.