Most Useful Guide to Fixing Shopify Inventory Issues

You’re hitting new milestones in sales, but is your Shopify inventory keeping up?

Growth is every Shopify merchant’s goal, but scaling introduces unique challenges that basic features of Shopify alone can’t address.

Critical tasks like syncing inventory across sales channels often result in errors and stock imbalances, while tracking product variants becomes more complex as your catalog grows. 

Add to that the complexities of managing suppliers, handling returns, and forecasting demand.

This is why your operations need a layer of advanced inventory features. By integrating Shopify inventory software, you can centralize your entire inventory, predict demand, automate key processes, and gain deep insights for timely interventions.

This article will elaborate on some common Shopify inventory issues, how inventory software can solve them, and a rundown of the top seven tools you can choose from. 

Common Shopify Inventory Issues

Shopify’s inventory features work well when you have just one sales channel, a small product catalog, and limited order volume, but as your business scales, Shopify quickly becomes inadequate. 

Here are 5 reasons why. 

1. Lack of in-built demand forecasting 

Shopify’s native features don’t include demand forecasting. This means merchants cannot predict future sales based on past performance, seasonality, or market trends unless they have the bandwidth to do complex calculations manually. 

Without accurate forecasts, you may risk overstocking slow-moving items or running out of popular products, both of which impact revenue and customer satisfaction.

2. No real-time stock visibility across sales channels  

Shopify’s inventory dashboard doesn’t record sales done outside Shopify. Items sold through other platforms or offline channels don’t automatically update in Shopify unless manually entered or maintained on a separate spreadsheet. 

This puts merchants at serious risk of overselling products they can’t fulfill and damaging customer trust and business reputation.

3. Absence of raw material management

The default Shopify features do not support raw material management for manufacturers. Businesses depend on external tools for ordering and tracking the components needed for production. 

This gap disrupts manufacturing processes and causes delays in fulfilling customer orders. 

4. Can’t manage purchase orders and suppliers 

Shopify doesn’t let you track purchase orders (POs) or manage supplier communications. 

Merchants often need to rely on third-party apps or manual methods to reorder products, which can lead to missed orders, stockouts, overordering, or missed opportunities to optimize supplier relationships.

5. Basic reports and analytics 

While Shopify offers some analytics, they are limited to high-level metrics like sales performance. The platform doesn’t provide detailed inventory reports, low-stock alerts, demand forecasting, or profitability tracking, making it harder to make accurate data-backed decisions. 

Why Shopify Inventory Software is the Solution?

Various inventory tools have emerged to tackle the common inventory issues faced by many Shopify merchants. These solutions bridge the gaps in Shopify's native features and add value in the following ways

1. Real-time tracking and visibility 

Inventory software gives you instant visibility into stock levels across all your sales channels. When an order is placed, your inventory is automatically updated, so you always have an accurate view of what’s available.

With this real-time sync, you can stay in the loop on any movement across your supply chain, prevent overselling, and eliminate the need to reconcile inventory manually. 

Prediko brings all your sales and inventory data together in one place, making it easy to manage multi-stores, multi-warehouses, bundles, and subscriptions.

2. Automation for efficient workflows 

Inventory software takes the manual work out of inventory tracking, reordering, and reporting. 

With automated workflows, you can save a number of hours and reduce team workload and scope of error while maintaining up-to-date inventory across all channels without constant monitoring. 

For instance, when a product's stock drops below a predetermined level (say, 10 units), the tool can automatically generate purchase orders, notify suppliers, and even calculate optimal reorder quantities based on historical sales data. 

Prediko's inventory software sends automated replenishment alerts and email reports, uses AI to create forecasting plans, and has a buying table that tells you what to buy, when, and in what quantities.

3. Integration with Shopify and other tools

Scaling businesses often rely on multiple tools and platforms. Inventory software acts as the headquarters or a centralized dashboard, connecting seamlessly with Shopify and other tools like QuickBooks, ShipHero, and marketplaces including Amazon and Walmart.

This makes information flow easier, lets you track sales, manage inventory, oversee distribution networks, and generate accurate reports while reducing admin workload and data discrepancies.

Prediko offers 40+ integrations with warehouse management systems, third-party logistics tools, and other business platforms for synched operations.

4. Advanced reporting and granular insights

An inventory software doesn't just do surface-level tracking, it reveals nuanced business intelligence. You can visualize sales trends, identify seasonal demand patterns, analyze product performance across different channels, and even predict future inventory. 

Tracking granular metrics like top-selling products, gross profit, return rate, and days of cover, help you make timely decisions on inventory levels, pricing, procurements, and promotions.

Prediko generates analytics on top-performing products, the number of purchase orders that are late or due for delivery, the percentage of the plan achieved for the week, SKUs in excess, etc. It also shows 90 metrics within the buying table for deep insights.

5. Prevention of stockouts and overstocking

Shopify inventory tools have evolved over time and now use predictive models and AI algorithms to anticipate future inventory based on historical data, seasonal trends, and sales patterns. These tools can predict possible stockouts weeks in advance, recommend ideal inventory levels, and even suggest markdown strategies for slow-moving products. 

Such proactiveness helps prevent out-of-stock situations, adjust procurement strategies, reorder accurate inventory levels, and reduce overstocking and unnecessary storage costs.

Prediko’s AI can distribute your revenue target across 12 months by analyzing historical sales data, seasonality, and growth trends. Its Buying Table suggests which products to buy, when, and in what quantities. 

6. Improved customer satisfaction

Inventory accuracy directly translates into customer satisfaction. By making products available when customers want them, you can reduce out-of-stock instances, minimize shipping delays, and bring in repeat business through reliable service delivery.

Up-to-date stock information also allows you to fulfill orders promptly, avoid negative reviews, and create a hassle-free shopping experience.

Top 7 Shopify Inventory Software for 2025

We will now review the seven best Shopify inventory software, comparing their features and pricing to help you pick one for your business.

1. Prediko 

Topping our list is Prediko, an inventory OS that lets omni-channel brands plan and order their stock easily. With focus on cutting down repetitive tasks and using AI for smarter decision-making, it unifies demand planning, supply planning, purchase order management, raw materials tracking, and in-depth reporting.

Its seamless integration with Shopify and over 40 other tools makes it a standout option for scaling businesses.

Key features 

• AI algorithm to create monthly forecasts based on your annual target, historical sales data, seasonality, and growth trends. Edit forecasts, buy the right amount with purchasing recommendations, and drill down your plan with 100+ filters. 

• Detailed analytics with metrics like top products’ performance, number of POs that are late or due for delivery, inventory retail value, percentage of the plan achieved this week, number of SKUs in excess, and more.

• Automated daily and weekly inventory alerts shared via email to prevent stockouts and overstocks. "Buy Now" nudges based on lead times, safety stock and stock cover units to prevent shipping delays. 

• Buying Table, in an Airtable UI helps plan your supply and suggests what you need to buy, when, and in what quantities for your Shopify store. It comes with 90+ metrics and health checks for all your SKUs. 

• Raw material management across multiple warehouses, including forecasting, bills of materials creation and tracking, made-to-stock production orders, and more.

• One-click purchase order generation based on Prediko’s real-time purchase recommendations. Create, review, and share your POs with suppliers using exports and in-app emails.

See Prediko in action:

2. Assisty 

Assisty is an inventory planning and management platform that removes the hassles from your inventory processes. It improves visibility across locations and automates replenishment and reporting, helping Shopify merchants save time and make faster, more informed decisions. 

Key features

• Unified inventory view across locations with location-specific stock levels, transfer suggestions, and forecasting 
• Automated reordering based on customizable parameters
• Demand forecasting based on historical sales, seasonality, and event planning 
• Analytics to track top-selling products, segment products, and align sales and inventory 
• Reports scheduling option and data syncing with Google Spreadsheets

Pricing 

Their pricing is based on your chosen Shopify plan. For the Advanced Shopify plan, pricing starts from $59 per store/month. They also offer a free plan for limited usage. 

3. Genie 

Genie is a collaborative and easy-to-use solution with capabilities to track, plan, order, and analyze inventory. It eliminates the manual spreadsheet processes, gives access to real-time data, and allows you to set up inventory workflows within minutes.

‍Key features

• Real-time inventory tracking across the entire product catalog
• Automated demand planning and forecasting for stock accuracy 
• Templated and custom reports to access insights like stockout risks, inventory distribution, sales velocity, overstocks, etc
• Create, manage, analyze, share, and export purchase orders
• Recommended reorder amounts based on sales data and desired coverage
• Save supplier details and track conversations with them 

Pricing 

There’s only one plan priced at $59 per month 

4. Qoblex

Qoblex is an inventory management software that lets you manage multiple aspects of the supply chain including manufacturing, forecasting, inventory, and fulfillment. It also offers a B2B eCommerce platform that can be easily integrated with your existing operations.

‍Key features

• One master inventory to connect multiple sales channels 
• Real-time inventory tracking across multiple warehouses and locations
• Automated workflows for procurement and manufacturing processes
• Order fulfillment in different currencies, prices, and terms
• Track metrics like stock on hand, profit margins, transaction history, sales, returns, etc

Pricing 

The base price is $149/month for up to 1,000 orders per month

5. Sumtracker 

Sumtracker’s inventory software automates routine tasks like multi-store inventory syncing, order management, and bundle tracking. It’s easy to set up and use, with responsive support available whenever you need assistance.

Key features

• Multichannel real-time inventory sync with a common inventory dashboard 
• Easy bundle management including the creation of bundles, inventory updates, and reports
• Create, send, and classify purchase orders, save supplier information, and automate cost calculations
• Inventory, forecasting, sales, and purchase reports for any time range 
• Location-wise low stock alerts via email and inventory movement logs for each SKU

Pricing 

Plans start from $49 per month for up to 200 orders

6. Inventory Planner

Inventory Planner’s straightforward platform helps you tackle Issues like overstocks, stockouts, forecasting, and data consolidation. It has a support team of former buyers and merchandisers who understand the common merchant challenges and provide expert-led onboarding, training, and support.

Key features

• Custom forecasting models for different products, locations, and warehouses
• Automated forecast adjustments for trends and marketing activities 
• Fully customizable reports with 200+ metrics like last sold date, overstock units, location performance
• Supplier management, buying recommendations, pre-set data for purchase orders
• Inventory purchasing and warehouse transfer recommendations 

Pricing 

Custom quote based on business needs 

7. SKULabs 

Lastly, we have SKULabs that brings your retail and wholesale stores, marketplaces, and brick-and-mortar sites into one app. In addition to inventory management, it powers fulfillment workflows with features like barcode scanning, label printing, and access to discounted shipping rates.

Features

• Monitor, sync, and manage stock levels across all sales channels, warehouses, and locations 
• Real-time tracking of inventory flow 
• Create cycle counts for up-to-date warehouse inventory 
• Barcode scanning for returns and stock transfers

Pricing 

Plans start at $299/mo for up to 1,000 orders 

How to Choose the Right Inventory Software for Your Shopify Store?

Now, these are a lot of options. To determine which inventory software is worth the investment for your business, use our “SMART” formula

1. S - Specific needs: Identify the exact blockers you are facing and align features, such as real-time sync, forecasting, or multi-store support. The software must address your pain points like stockouts or manual tracking.

2. M - Multi-channel integration: Opt for software that integrates with Shopify, marketplaces, accounting tools, and shipping platforms while giving you a real-time view of the consolidated data. The connectivity ensures you’re able to scale easily without the switching costs.

3. A - Automation: Look for tools that automate repetitive tasks like inventory syncing, replenishment, purchase order creation, forecasting, or inventory counting. Automation saves both time and money. 

4. R - Reporting & analytics: Prioritize platforms that offer reports and insights beyond what Shopify offers like low stock alerts, profit margins, inventory retail value, purchase orders due for delivery, etc.

5. T - Training & support: Choose software that is backed by excellent customer support and onboarding assistance. Ensure it’s easy to set up and offers enough resources to train your team quickly.

Leave Your Inventory Issues Behind with Inventory Software 

While Shopify is great for running your online store, managing inventory can still be tricky. 

An inventory software not only solves common Shopify inventory issues but offers much more.

It connects seamlessly with Shopify to give you real-time stock visibility, improve order management across channels, and automate restocking. This allows you to reduce human error, speed up order fulfillment, and gather insights for smart inventory planning.

Wondering if it’s time for you to switch to dedicated inventory software? Look for these signs.

• Frequent stockouts or tied-up capital due to overstocking 
• Difficulty in tracking inventory across multiple locations
• Slow or inaccurate order fulfillment processes
• Errors in inventory counts or data entry due to their manual nature
• Limited visibility into sales trends or stock performance

Among all the above options, Prediko outshines as a multi-dimensional inventory tool for businesses of all shapes and sizes. 

Over 500+ Shopify brands trust Prediko for inventory management. Become one of them by taking a free 14-day trial.