Inventory software and online store compared
You have a shop and an online store, and the question is simple: how do you keep stock correct in both? On vendors' sites every solution looks suitable, but the real difference shows in three places: who holds the correct stock level, how many integrations sit in between and how many bills arrive each month.
Short answer: if you only sell online, an e-commerce platform is usually enough. A business with a shop and an online store needs either a POS system with an integration or one application. The more channels and services you have, the more one database wins.
Below I compare five common setups. Prices come from vendors' public pages as of 1 November 2026 and may change.
Comparison at a glance
| Setup | Example | Where the correct stock level is | Integrations | Works well for |
|---|---|---|---|---|
| Online store + plugin | WooCommerce + ATUM | In the online store | 0–1 | Mostly online sales |
| E-commerce platform + its own POS | Shopify + POS | On the platform | 0 | Retail focus, no services |
| POS system + online store | Erply + Shopify | In the POS system | 1 | Several shops |
| Online store + separate stock program | Online shop + Zoho Inventory | In the stock program | 1–2 | Many orders and a separate warehouse |
| One application | NUNDINAE | In one database | 0 | Online store, shop and services together |
1. WooCommerce and a stock plugin
WooCommerce is free, but the shop needs hosting, a theme and add-on modules. The online store keeps the stock level itself, and this can be extended with plugins. Paid modules are often priced per year; WooCommerce Subscriptions, for example, costs €252 a year in the official store.
Risk point: every module is a separately updated part. The POS isn't an integral part of the system either, but comes as another add-on. I wrote more in WooCommerce alternative.
2. Shopify and its POS
In Shopify the online store and stock are together, and the POS is from the same family. Basic costs $39 a month with monthly billing and $29 a month with annual billing; Grow costs $105 and $79 respectively. POS Pro is an add-on at $89 a month per location. With an external payment provider, a transaction fee of 2% (Basic) or 1% (Grow) is added.
Risk point: booking services isn't its main focus, so it has to be added as an app. See also Shopify alternative for an Estonian business.
3. POS system and online store
If shops are at the centre, the correct stock level can be in the POS system and the online store gets its data from there. In Erply's public price list, the simple package starts at $49–59 per shop per month and the multi-channel package at $179–199 per shop. The latter includes a Shopify integration, among other things. The amount depends on the billing period.
Risk point: the online store is still a separate system with its own monthly fee, and an integration runs between the two. When it stops, stock levels don't match. A good solution for a chain of several shops, but often too heavy for a small business.
4. Online store and a separate stock program
A stock program such as Zoho Inventory keeps quantities and orders. Standard costs $29 a month with annual billing for up to 500 orders, Professional $79 for up to 3,000 orders. In Estonia, the stock modules of accounting programs are also used for this. Ask the vendor about their price and the fee for an online store integration.
Risk point: two product catalogues. If the SKU differs between the two, the integration can't find the product and you only notice the error when the stock level is already wrong. I explain why this happens in online store and stock sync.
5. One application
I built NUNDINAE on this model. The online store, inventory management, POS and bookings use one database:
- There is no integration, because there is nothing to sync.
- A till sale, an online order and receiving goods all change the same stock level.
- An unpaid order holds the goods and releases them on its own when it expires.
- A service booking, the materials used and a product bought to take home are on the same invoice.
Risk point: there are limits here too. NUNDINAE isn't a logistics system for several warehouses and large flows of goods, and it doesn't replace an accounting program. The price comes as a quote, because it depends on the modules and the size of the migration. Hosting, Montonio fees and SMS messages are added according to use.
How to choose
Answer four questions:
- Do you have a physical warehouse or shop? If not, start with an ordinary online store.
- How many shops do you have? With many shops, look at a POS system.
- Do you also sell appointment-based services? If so, the advantage of one application is greatest.
- How much time goes on moving data around by hand? Count that cost along with the monthly fees. I made a worked example for this.
Frequently asked questions
Is an integration always bad?
No. A well-made integration works for years. It's just that every integration is one more part to monitor, update and fix when something goes wrong.
How big does a business have to be to need a real warehouse management system?
If you have several warehouses, shelf addresses, pickers and many orders a day, you probably need a specialised system. A small or medium-sized shop usually gets by with something simpler.
Can I move from one setup to another?
Yes, if the data can be exported. See how data migration works.
Does one application suit your business?
Describe what you sell and what you work with now. Order NUNDINAE or ask for a demo. If another solution suits you better, I'll tell you honestly.
