Accounting System Setup, Software Migration and Integration Services in Canada
Bestax designs, sets up and connects the accounting system your business runs on. We help you choose the right software, build the chart of accounts and tax codes, migrate your data from spreadsheets, QuickBooks Desktop or another cloud tool, connect bank feeds, payroll, e-commerce and payments, and train your team so the numbers are right every month and every CRA filing comes straight out of the system.
Speak Directly with an Expert
- 10+YEARSof experience
- 1,000+ Businesseslaunched with Bestax
- 35+ Qualified Professionalsprofessional accountants
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Trusted by businesses across Canada to stay compliant, organized and financially confident.
Five rules your accounting system has to meet in 2026
Six years of records, in a format the CRA can read. Electronic records must be kept for six years from the end of the last tax year they relate to, in an electronically readable format with working backups.
Records kept on servers outside Canada are not "kept in Canada". The CRA's own words. If your cloud provider hosts your data abroad, you need the CRA's written permission or a system that keeps a copy in Canada.
Every GST/HST return is filed electronically. All registrants except charities and selected listed financial institutions. Paper filing costs $100 for the first return and $250 for each one after.
More than five T4 slips means electronic filing. Since January 2024 the threshold dropped from 50 to 5, with penalties from $125 for a small payroll.
QuickBooks Desktop Pro and Premier are no longer sold to new Canadian customers. Sales stopped on 15 April 2025, and services for the 2023 versions ended on 31 May 2026. If you are still on Desktop, the migration to QuickBooks Online needs planning, not panic.
Not sure whether your current setup passes? Send us a screenshot of your chart of accounts and a description of your software, and we will tell you within two business days what needs to change, at no cost.
Our Strength in Numbers
- 10+Years setting up and running accounting systems for Canadian businesses
- 35+Qualified professionals in accounting, bookkeeping and systems
- 2Offices, Mississauga and Dubai
- 6 daysOpen every week, Monday to Saturday, 9am to 8pm
Every setup is built by an accountant, not a software reseller, and reviewed by a second professional before you go live. We are an ACCA Approved Employer and an ICAEW Approved Employer.
Signs It Is Time to Set Up or Replace Your Accounting System
Most businesses call us for one of these reasons. If two or more apply, the cost of waiting is already higher than the cost of the project.
You run the business on spreadsheets or a bank app.
Fine for the first few months, but there is no audit trail, no GST/HST report and no way to hand the CRA six years of records if asked.
You are still on QuickBooks Desktop Pro or Premier.
New subscriptions ended in April 2025. Existing subscribers can keep using their version while the subscription is active, but bank feeds, payroll and support for older releases are being switched off version by version.
Three tools that do not talk to each other.
Invoicing in one app, expenses in another, payroll in a third, and the bookkeeper re-typing everything at month end.
Bank reconciliations are months behind.
Unreconciled accounts are the first thing an external auditor, a lender or the CRA notices.
You sell online or in more than one province.
Marketplace settlements, HST at 13 percent in Ontario and 5 percent GST in Alberta, PST in BC, QST in Quebec. A system set up for one province gets the others wrong.
You hired your first employees.
Payroll deductions, T4s and remittances by the 15th need to flow from the system, not from a calculator.
Year end takes weeks and costs more each year.
Your accountant is rebuilding your books instead of reviewing them.
You are growing, raising money or preparing to sell.
Buyers and lenders ask for system-generated reports with a clean audit trail. A rebuild under deadline is the most expensive kind.
Canadian small businesses already spend an average of 256 hours a year, about 32 business days, on regulatory paperwork according to the CFIB's 2025 Red Tape Report. A well-built system is the single biggest way to cut that number.
Choosing the Right Accounting Software for a Canadian Business
You do not need to know the software before you call. We choose it with you, based on your size, industry, transaction volume, GST/HST and payroll needs, the apps you already use and where you are heading. The table shows what we look at, verified against each vendor's Canadian site in August 2026. Prices change often, so we leave them to the vendors and to our Canadian accounting software comparison.
QuickBooks Online (EasyStart, Plus, Advanced)
- Best fit
- Most owner-managed businesses, service firms and retailers; the widest choice of Canadian bookkeepers and app integrations
- Canadian payroll
- Built in: QuickBooks Payroll files and remits to the CRA and Revenu Québec
- Watch out for
- Plan limits on users and features; Desktop Pro and Premier no longer sold to new customers, so Desktop users migrate here
Free or paid? Wave Starter and Zoho Books Free are real products for a business with a handful of transactions a month. Once you need bank feeds, receipt capture, payroll, inventory or more than one user, a paid plan pays for itself in the first month of saved bookkeeping time. Starting free and upgrading later is a sound plan as long as the chart of accounts is built properly from day one, because that is what you cannot cheaply change later.
Around the ledger. Receipt capture with Dext or Hubdoc, payroll with Wagepoint, Payworks, Rise People, ADP Canada, Dayforce Powerpay or Humi, and connections to Shopify, Amazon, Square, Stripe and your point of sale. We set up the whole stack, not just the ledger.
What Our Accounting System Setup and Integration Service Includes
Discovery and System Design
We review how money moves through your business today: invoicing, purchasing, inventory, payroll, sales tax, approvals and reporting. You receive a written design covering the software, the chart of accounts, the integrations, the data to migrate, the user roles and the reports, before anything is built.
Moving From QuickBooks Desktop to QuickBooks Online in Canada
This is the most common migration we run in 2026, and the timing is set by Intuit rather than by you.
What changed
QuickBooks Desktop Pro, Premier and Desktop Payroll stopped being sold to new Canadian subscribers on 15 April 2025. QuickBooks Desktop Enterprise is still sold.
Existing subscribers can keep using their current version for as long as the subscription is active, but services for the 2023 versions (payroll, bank feeds, payments, support and security updates) were discontinued on 31 May 2026, and each later version has its own date.
Intuit's recommended destination is QuickBooks Online, using its migration tool or a fresh start.
What moves and what does not
Moves across
Needs rebuilding or a decision
Chart of accounts, customers, suppliers, items, open invoices and bills
Memorised reports, custom templates and some custom fields
Transaction history within the tool's limits
Inventory assemblies and advanced job costing, which work differently online
Payroll year-to-date balances, when planned properly
Bank feed connections and rules, which must be re-established
Balances reconciled to the last filed GST/HST and T2
Third-party Desktop add-ons, replaced with online equivalents
When to move. The first day of a fiscal year or the first day of a GST/HST reporting period gives the cleanest cut-over, with the old file kept read-only for the six-year retention period. A mid-year move is possible; it just needs a reconciled cut-over date.
A fresh start is sometimes better. A Desktop file with years of unreconciled items, unused accounts and duplicate names is a liability to import. We compare a conversion with a clean rebuild plus opening balances and recommend the one that costs less over the next three years, not the next three weeks.
Setting Up the System to Satisfy the CRA
A system that produces the right filings is the difference between a five-minute reply to a CRA letter and a five-week reconstruction. Verified against CRA guidance in August 2026.
CRA requirement: Keep records for six years from the end of the last tax year they relate to. How we build it in
Archive of migrated history in a readable format; closed periods locked; retention schedule documented
CRA requirement: Records must be kept in Canada unless the CRA gives written permission; records on servers outside Canada accessed from Canada do not count as kept in Canada. How we build it in
We check where your provider hosts Canadian data, keep a Canadian copy of exports and backups where needed, and prepare the written request to your tax services office when a foreign-hosted system is the right choice
CRA requirement: Electronic records must be accessible and useable by CRA auditors, with tested backups. How we build it in
Export routines, backup schedule with periodic restore tests, and a documented backup location in Canada
CRA requirement: Paper documents may be imaged and the paper destroyed if imaged to the national standard. How we build it in
Receipt capture configured to store legible images with the transaction
CRA requirement: GST/HST returns filed electronically by all registrants except charities and SLFIs. How we build it in
GST/HST codes by province, return prepared from the system and filed through CRA-approved channels
CRA requirement: Input tax credit documentation by invoice size (under $100, $100 to $499.99, $500 and over). How we build it in
Supplier records and receipt capture set to hold the registration number and required fields
CRA requirement: T4 and other slips filed electronically when more than five are issued. How we build it in
Payroll platform with CRA-ready slips and electronic filing
CRA requirement: Payroll remittances by the 15th of the following month for regular remitters. How we build it in
Remittance liabilities tracked in the ledger with calendar reminders
CRA requirement: CRA payments of $10,000 or more made electronically. How we build it in
Online banking or CRA My Payment set up and documented for the bookkeeper
CRA requirement: Single CRA sign-in and Business Registration Online through your CRA account since 14 July 2026. How we build it in
CRA account access organised for the owner and authorised representative, with our firm added through Represent a Client
Data Security, Privacy and Where Your Data Lives
Owners ask three questions, and the honest answers are these.
Is cloud accounting secure? The major platforms encrypt data in transit and at rest and are audited to recognised standards. The weak point is almost always the login. We follow the Canadian Centre for Cyber Security's baseline controls for small and medium organisations: two-factor authentication on every financial account and admin login, unique user IDs, admin rights limited to one or two people, leavers removed the day they go, and backups with long-term copies stored offline and tested.
Can our data be stored outside Canada? For privacy law, yes with safeguards: PIPEDA does not prohibit sending personal information to another country for processing, provided you use contracts to ensure comparable protection and tell customers it may happen. Quebec's Law 25 goes further and requires a privacy impact assessment before personal information is communicated outside Quebec, and before any project to acquire, develop or redesign an information system. For tax law, the CRA rule above applies regardless of privacy law. We handle both.
Who can see what? Roles are set so sales staff see invoices and not payroll, bookkeepers post but do not approve their own payments, and the owner sees everything. The audit trail records every change by user and time.
How the Project Runs
Free consultation, 30 minutes.
We learn how the business works, what software and spreadsheets you use, where the pain is and what deadlines are coming.
Discovery and design, week 1.
Document review, a walkthrough of your current process and a written system design with a fixed price.
Build, weeks 2 to 3.
Software set up, chart of accounts, tax codes, templates, user roles and integrations configured and tested.
Migration and reconciliation, weeks 2 to 4.
Data mapped, imported and reconciled to your last filed returns and statements; cut-over date agreed.
Training and go-live, week 4.
Team trained, procedures guide issued, old system set to read-only.
Support and review, days 1 to 30 after go-live.
Questions answered the same day, first month end and first GST/HST return reviewed together.
How long does it take? A basic setup for a small business runs two to four weeks. A migration with several integrations and years of data runs six to eight weeks. We give a dated plan at the design stage and hold to it.
What Accounting System Setup Costs
One written quote after the free consultation, and that is the number you pay. The quote depends on the software chosen, the volume and condition of the data to migrate, the number of integrations, the number of users to train and whether backlog cleanup comes first. Software subscriptions are paid by you to the vendor, so there is no markup and you own the account.
A note on grants. The federal Canada Digital Adoption Program grant that funded software projects closed to new applications in early 2024 and has not been replaced, and Ontario's Digital Main Street grant portal is also closed. We will tell you if a live program applies to you; we will not sell the project on a grant that no longer exists.
Why Businesses Choose Bestax for Accounting System Setup
Accountants First, Software Second
We are not a reseller earning commission on one platform. We choose the system that fits and then run the books, payroll, GST/HST and corporate tax on it, so the setup is built by the people who will use it.
Built for the CRA From Day One
Six-year retention, records-in-Canada, e-filing thresholds and input tax credit documentation are designed in, not bolted on after the first review letter.
Migration Without Lost Transactions
Every migration is reconciled to your last filed returns before go-live. No doubled invoices, no missing bills, no opening balance nobody can explain.
Training That Sticks
Owners and bookkeepers are trained on their own data, with a written month-end guide, and we stay on for the first month end and the first filing.
One Firm for What Comes Next
Bookkeeping, monthly and quarterly reporting, payroll, GST/HST returns and corporate tax, all from the system we set up.
On Site in the GTA, Remote Across Canada, and a Dubai Office
Hands-on setup in Mississauga, Brampton, Oakville and Toronto, remote implementation for every province, and a team in Dubai for owners with businesses on both sides.
Who We Help
Setup Mistakes We Fix Every Month
Each of these is checked before go-live on every system we build.
A chart of accounts copied from a template.
Two hundred accounts nobody uses and none of the ones the owner actually needs.
One sales tax code for every province.
HST charged to Alberta customers, GST only charged to Ontario ones, and a reassessment either way.
Bank feeds with no rules and no review.
Transactions posted to "uncategorised" for months, then guessed at year end.
Migrating everything.
Ten years of history imported with every historic error, when two clean years and an archive would have done.
Payroll outside the ledger.
Remittances and T4s reconciled by hand, if at all.
Everyone is an admin.
No approval limits, no audit trail worth reading, and a resigned employee with live access.
Foreign-hosted data with no Canadian copy.
Fine until the CRA asks for records and the answer is a login on a server in another country.
No backup ever tested.
A backup that has never been restored is a hope, not a backup.
Rules and Facts at a Glance (Verified August 2026)
- Where it stands
- Six years from the end of the last tax year the records relate to
- Source
- CRA, Keeping records, updated 3 August 2026
- Where it stands
- Must be kept in Canada unless the CRA gives written permission; records on foreign servers accessed from Canada are not kept in Canada; request permission by writing to your tax services office
- Source
- CRA, Keeping records
- Where it stands
- Electronically readable, accessible and useable by CRA auditors; backups restorable and periodically tested
- Source
- CRA Information Circular IC05-1R1
- Where it stands
- Mandatory for all registrants except charities and SLFIs; $100 then $250 penalties
- Source
- CRA, How to file, 2025
- Where it stands
- Mandatory when more than five slips are issued; penalties from $125 for 6 to 50 slips
- Source
- CRA, Filing information returns electronically, updated 21 July 2026
- Where it stands
- Required for CRA payments of $10,000 or more; $100 penalty per failure
- Source
- Income Tax Act s. 162(7.4); Excise Tax Act s. 278(3)
- Where it stands
- Single sign-in for My Account, My Business Account and Represent a Client since 15 January 2025; BRO only through a CRA account since 14 July 2026
- Source
- CRA tax tips, January 2025 and June 2026
- Where it stands
- Pro, Premier and Desktop Payroll no longer sold to new subscribers since 15 April 2025; Enterprise still sold; 2023 versions' services discontinued 31 May 2026
- Source
- Intuit Canada
- Where it stands
- Consumer-Driven Banking Act in force; regulations pre-published 27 June 2026 with comments to 26 August 2026; oversight by the Bank of Canada; accreditation is the first phase
- Source
- Department of Finance; Bank of Canada
- Where it stands
- No mandatory business-to-business e-invoicing in Canada
- Source
- Department of Finance consultations; no CRA mandate
- Where it stands
- 48 percent of Canadian businesses with five or more employees used cloud computing in 2023, the most used technology
- Source
- Statistics Canada, September 2024
- Where it stands
- 256 hours, about 32 business days, a year per business; $51.5 billion in total compliance costs
- Source
- CFIB Red Tape Report, January 2025
- Where it stands
- Two-factor authentication wherever possible, especially financial and cloud admin accounts; long-term backups offline and tested
- Source
- Canadian Centre for Cyber Security, Baseline Controls V1.2
Our Other Services
The system is the foundation. These are the services that run on it.
Accounting and Bookkeeping: monthly books kept in the system we built.
Backlog Accounting: catch-up before migration.
Monthly and Quarterly Financial Reporting: the dashboards and packs the setup makes possible.
Payroll Services: deductions, remittances and T4s from the integrated platform.
GST/HST Return Filing and GST/HST Registration: tax codes to returns.
Corporate Tax Return Filing: the T2 prepared from clean, system-generated statements.
Internal Audit: testing the controls the system enforces.
Helpful guides: Canadian accounting software comparison, what accounting automation actually does, how to prepare a bank reconciliation, bookkeeping for small businesses in Canada, tracking business expenses and how long to keep tax records.
Our Success Stories
I was worried about company due to some bookkeeping errors done by the company i hired before bestax, Bestax made it simple and straightforward. They handled and corrected everything, kept me informed,. I can’t thank them enough for taking care of it all.
Google review 1 of 4: Bryant Phillip
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Frequently Asked Questions
The one that handles your GST/HST by province, your payroll if you have staff, the apps you already use and the number of users you need, at a price that fits. For most owner-managed businesses that is QuickBooks Online or Xero; for invoicing-led consultants FreshBooks or Wave; for inventory-heavy or multi-user operations Sage 50. We recommend after a 30-minute call, and we are not paid by any vendor.
Yes. Wave Starter and Zoho Books Free are genuine products for a business with a few transactions a month. The limits arrive quickly: Wave's free plan no longer includes bank feed import or receipt capture, and none of the free plans include payroll. Start free if you like, but let us build the chart of accounts properly first, because that is the part you cannot cheaply fix later.
Not today if your subscription is active, but the direction is set. Pro, Premier and Desktop Payroll have not been sold to new Canadian customers since April 2025, and services for the 2023 versions ended in May 2026. Plan the move for your next fiscal year start, keep the old file read-only for six years, and decide with us whether to convert the file or rebuild clean.
Only if the current system is failing you. If it handles your tax, payroll and reporting and your team uses it well, we improve the setup rather than replace it. If you are re-typing data between tools, reconciling months late or building reports in spreadsheets, a change usually pays for itself within a year.
Two to four weeks for a basic setup, six to eight for a migration with several integrations and years of data. You keep invoicing and paying bills throughout; we build in parallel and switch over on an agreed date, usually the first day of a period.
That is the point of using an accounting firm to build it. Tax codes by province, invoice fields for input tax credits, six-year retention, tested backups, electronic filing of GST/HST returns and T4s, and the records-in-Canada rule are all handled in the design. The table above sets out each rule and how we meet it.
Most cloud platforms host Canadian customers on servers that may be outside Canada. Privacy law allows that with contractual safeguards and customer notice, and Quebec's Law 25 requires a privacy impact assessment first. Tax law is stricter: the CRA does not treat records on foreign servers accessed from Canada as records kept in Canada, so we either keep a Canadian copy of your data and backups or prepare the written request for CRA permission. Either way, you will know before go-live.
Yes. Payroll platforms, e-commerce and payment settlements, receipt capture, point of sale and CRM tools are connected where the integration is reliable and replaced with a better tool where it is not. Bank feeds are connected and secured with two-factor authentication; note that Canada's open banking system is not live yet, so feeds still run through aggregators.
Most of our clients are not. Training is done on your own data, in plain language, with a written month-end guide, and we stay for the first month end and the first GST/HST filing. Our Mississauga office also trains on site across the GTA.
You receive one fixed written quote after the consultation. It covers design, build, migration, integrations, training and 30 days of post-launch support. Software subscriptions are paid directly to the vendor with no markup. After the first month, you can keep us on a retainer for the books and support, or call us as needed. We will also tell you plainly that the federal software grant program closed in 2024, so the project is priced to stand on its own.