San Diego County Bookkeeper Talk to a bookkeeper

Short answer: Biotech bookkeeping in San Diego codes research spend by program, tracks each grant's budget and drawdowns apart from investor cash, and records financing rounds as they close. Each month you get burn, runway and a clean trial balance. The coding also gives your CPA what they need for the R&D credit and the Section 174A deduction.

A lab spends money in ways a normal P&L hides

A preclinical company on Torrey Pines Mesa can go two or three years with no product revenue. Money comes in from a seed round, a SAFE, an NIH or SBIR award, or a partner milestone. Money goes out to lab rent, CRO invoices, reagents, equipment leases and a payroll full of scientists.

If all of that sits in one bucket called research, nobody can answer the questions that matter. How much did the lead program cost this quarter? How much grant money is left to draw? How many months of cash are left if the next round slips?

What the books track for a life sciences company

  • Research spend split by program or compound, using classes in QuickBooks Online or tracking categories in Xero
  • Each grant or contract set up with its own budget, so spending and drawdowns can be compared line by line
  • Grant receipts kept apart from equity funding, so restricted money is not confused with operating cash
  • CRO, CMO and consultant invoices matched to the work order or statement of work they belong to
  • Lab equipment recorded as fixed assets, with leases and financed purchases on the balance sheet
  • Financing events such as priced rounds, SAFEs and convertible notes recorded when they close
  • Monthly burn and runway, built from the reconciled books rather than a separate spreadsheet

Grant and milestone money

Federal awards come with rules about what costs are allowed and how they are reported. Your grants administrator or CPA owns the compliance side. The bookkeeping job is to make sure every dollar charged to an award is coded to it, supported by an invoice or a payroll record, and easy to pull when a drawdown or report is due.

Partner deals often pay on milestones. A payment can arrive months after the work, or before it. The books record when the cash came in and flag it for your CPA, who decides how the revenue is recognized.

Research spend and the tax return

Clean research coding matters at tax time for two reasons. The federal research credit is claimed on Form 6765, and a qualified small business can elect to apply up to $500,000 of it each year against payroll tax. That is useful for a company with losses and no income tax to offset.

Second, the One Big Beautiful Bill Act added Section 174A, which lets businesses deduct domestic research costs in the year they are paid for tax years beginning after December 31, 2024. Your CPA makes the elections. The books need to show which wages, supplies and contract research were domestic research, by year.

Tax treatment is your CPA's call. The books give them clean, coded numbers to work from.

Burn, runway and the next raise

Investors and board members ask for the same few numbers every quarter: cash on hand, monthly net burn and months of runway. When the books close on time each month, those numbers come straight from reconciled accounts.

Diligence is harder. A lead investor's team will ask for monthly financials, a cap table that ties to equity on the balance sheet, and support for large vendor balances. Books kept current all along turn a stressful data room into a few exports.

How the monthly work runs

  1. Collect Bank and card feeds, payroll reports, CRO invoices and grant budgets come in each month.
  2. Code Every expense is tagged to a program, and grant costs are tagged to their award.
  3. Reconcile Bank, card and loan accounts are matched to statements, and prepaid and accrued costs are adjusted.
  4. Report You get a P&L by program, a balance sheet, burn and runway, and a grant spend summary.

Signs the books are behind the science

  • Runway is calculated from the bank balance, not the books
  • Grant spending lives in a separate spreadsheet that does not tie to the books
  • A CRO invoice for six months of work was expensed in one month
  • The SAFE you signed last year is not on the balance sheet
  • Your CPA asked which wages were research wages and nobody knew

Biotech life sciences by city

Where we work

We keep books for businesses across the City of San Diego, North County, the South Bay and East County.

Questions

Do you prepare grant reports or handle grant compliance?

No. The books are set up so your grants administrator or CPA can pull spending by award quickly. Compliance decisions and filings stay with them.

Can you clean up books before a fundraise?

Yes. A cleanup or catch-up brings past months current, ties equity to your cap table and gets the books ready for an investor's diligence list.

Do you calculate the R&D tax credit?

The bookkeeping team codes research spend so the numbers are ready. The partner team also works on R&D credit studies if you want that handled.

We are a two-person company in an incubator. Is it too early?

No. Setting up program and grant tracking from the first invoice is much easier than rebuilding it after a round closes.

Sources

Talk to a bookkeeper

Tell us where your books stand. A bookkeeper reads it and replies to set up a short call.

  • No cost to ask.
  • You get a real person, not a sales sequence.
  • One month behind or three years behind, the first call is the same.