Integrate Amazon with QuickBooks Online
Amazon sends settlement summaries. QuickBooks expects structured journals. NeonPanel maps every line type, posts settlement-sized summaries with true FIFO COGS, and keeps detail in NeonPanel for audit.
Unified system
- Accounting
- Inventory
- Forecasting
- AI access
Trusted by 200+ ecommerce teams
What your books look like without a proper integration
Native sync moves data; it rarely lands in accounts you can defend. Five patterns we see:
- Amazon settlements arrive as lump sums — no fee breakdown, no category mapping.
- FBA fees, referral fees, and refunds land in a catch-all account.
- COGS are either missing or estimated using averages.
- Inventory values in QuickBooks do not reflect what is actually in your warehouse.
- Your accountant spends the first hour of every month untangling the same problems.
Clean entries, every time
How it works
Connect Your Accounts
OAuth Seller Central and QuickBooks Online. No shared passwords.
Configure Your Mapping
Point fees, refunds, COGS, tax, and revenue types at the right accounts.
Automate & Sync
Each settlement posts payouts, fees, inventory moves, and COGS on the schedule Amazon closes.
Most sellers discover the rest after they see the P&L
Clean Amazon → QuickBooks is the foundation. Same ledger supports multi-warehouse inventory, replenishment, FBA shipment automation, and SKU-level margin. Start with accounting; add modules as you scale.
Looking for the broader picture? See ecommerce accounting on NeonPanel or compare to reconciliation-only tools.
Your accountant will thank you
14-day free trial. No card required.
- ✔ Faster month-end close.
- ✔ Accurate profit margins.
- ✔ Zero manual reconciliation.
Amazon Seller Central to QuickBooks Online — the actual integration
Goal: each Seller Central settlement becomes one mapped QuickBooks Online journal (plus COGS), sized to the bank deposit, with line detail retained in NeonPanel. Steps below match how operators and accountants set this up.
Step 1 — Connect Seller Central via SP-API
OAuth through Seller Central to Selling Partner API (SP-API). NeonPanel ingests settlements, orders, FBA fees, ads, tax, refunds, reimbursements, and inventory movements.
Step 2 — Map the Seller Central transaction set to your QuickBooks Chart of Accounts
Typical QuickBooks Online mapping for the Seller Central set:
- Sales → revenue accounts split by SKU group, product line, or marketplace.
- Referral fees, FBA fulfilment fees, FBA storage, long-term storage, removal, return processing, inbound placement → separate fee accounts so each is reportable.
- Advertising spend → marketing expense, optionally split by campaign type.
- Refunds & reimbursements → contra-revenue and other-income accounts respectively.
- Marketplace-collected sales tax → held separately from seller-collected tax to keep liability accounts clean.
- FBA inventory movements → inventory asset adjustments and COGS entries.
Step 3 — Post one summary journal per settlement
One summary journal per settlement period keeps QuickBooks Online fast. Line items stay in NeonPanel. The journal total matches the Amazon deposit so bank rules clear in one step.
Step 4 — Attach true FIFO COGS
COGS on each summary uses true FIFO from purchase price plus landed cost (freight, duties, insurance), so margin tracks batches instead of a static average.
Step 5 — Backfill history, then run continuously
Backfill from a chosen go-live date, then let new settlements post on their own cadence.
Pair this with multi-warehouse inventory tracking, forecasting & replenishment, and ecommerce accounting on NeonPanel for the full operating picture.
Sync Everything
Catalogs
Including Products, Services, Customers, Vendors, and Currencies
Charts of Accounts
Use the default Chart of Accounts tailored for Amazon sellers or customize your own
Bills
Bills, purchase orders, and expenses synced in real-time
Invoices
Precise Cost of Goods Sold (COGS) calculated using the First-In, First-Out (FIFO) method
Four channels for the same instrument layer
NeonPanel's structured ledger, batch-level COGS, and shipment-level inventory reach your team through MCP, Claude, Slack agents, or Viktor. Pick the surface that matches how you work.
Direct MCP
Build custom agents in Cursor, Claude Code, or your own stack against the NeonPanel MCP server.
Set up MCP → For analysts & operatorsClaude plugin
Eight specialist agents in Claude Code or Cowork — routing and MCP tools included.
Connect Claude → For teams in SlackAgents in Slack
@mention Dorian, Marta, Nina, and the full default roster directly in Slack — same agents as Claude.
Open Slack agents → General coworkerViktor in Slack
One @mention for routing — Viktor picks the domain when you prefer not to choose an agent.
Meet Viktor →Recommendations land on real FIFO batch costs, not industry averages.
Flexible Pricing Plans
Choose the plan that fits your business needs
Essentials
Includes 10,000 orders/month · additional orders billed separately
Perfect for growing businesses
- ✓ One Amazon Seller Account
- ✓ Flexible Landed Cost Distribution
- ✓ Automated COGS Calculations
- ✓ QuickBooks & Xero Integration
- ✓ Unlimited Users & Roles
Professional
Includes 10,000 orders/month · additional orders billed separately
For multi-entity & multi-warehouse operations
- ✓ All Essentials Features
- ✓ Custom Chart of Accounts
- ✓ Multi-Entity Accounting
- ✓ Multi-Warehouse Inventory
- ✓ FBA, AWD & ASDN Shipments
- ✓ Accounting & Logistics Agents
Amazon Seller Central to QuickBooks — Frequently Asked Questions
Authorise NeonPanel against Amazon Seller Central via the Selling Partner API and against QuickBooks Online via OAuth. Choose how Amazon transaction types should map to your QuickBooks Chart of Accounts, then enable the sync. NeonPanel posts one summary journal per Amazon settlement, with true FIFO COGS attached, sized to match the bank deposit.
Every FBA fee type — fulfilment, storage, long-term storage, removal, return processing, inbound placement — is categorised separately and posted to its own account in QuickBooks Online. That makes channel-level and SKU-level margin analysis meaningful instead of dumping everything into a single 'Amazon fees' bucket.
Customer refunds are posted as contra-revenue against the original sales account so net revenue stays accurate. Amazon reimbursements (lost or damaged inventory) are posted to a dedicated other-income account so they are not confused with sales.
Yes. Marketplace-collected sales tax (where Amazon remits on your behalf) is held in a separate liability account from seller-collected tax to keep your QuickBooks liability records clean and audit-ready.
NeonPanel calculates COGS on a true FIFO basis using actual purchase costs and landed costs (freight, duties, insurance) for each inbound batch. The COGS posted alongside each Amazon settlement reflects what the inventory really cost — not an average.
Yes. Multiple Seller Central marketplaces (US, UK, EU, CA, etc.) and multiple seller accounts can be connected and rolled up into a single QuickBooks Online company. Channel-level reporting is preserved using QuickBooks classes or locations.
Yes. Settlements post in their native currency and respect QuickBooks Online's multi-currency configuration so foreign currency gain/loss is handled inside QuickBooks rather than estimated in spreadsheets.
Yes. NeonPanel can backfill historical Amazon Seller Central data into QuickBooks Online from a chosen start date so books are complete from day one of the integration.
Yes. Professional plans include onboarding calls. The team works alongside your accountant to configure NeonPanel, the Amazon connection, and the QuickBooks Chart of Accounts mapping so the integration matches your business structure.