Running a bakery means keeping recipes, ingredients, production schedules, and customer orders in sync while also meeting strict compliance requirements. The best bakery enterprise resource planning (ERP) software brings these moving parts into one platform, giving bakeries clear control over inventory, batch tracking, and sales.
Unlike generic systems, bakery-focused ERPs manage perishable goods and recipe-driven production directly. They help bakeries monitor expiration dates, control costs, and plan for growth without losing track of daily operations.
In this article, you’ll find the top platforms that support bakery operations, from ingredient sourcing to customer delivery.
What is Bakery ERP Software?
A bakery ERP software helps bakeries manage and streamline all aspects of their operations. It integrates inventory purchasing, ingredient tracking, production scheduling, sales, and customer management into one platform. By keeping these workflows connected, the system reduces errors, prevents unnecessary spoilage, and ensures compliance with food industry regulations.
Modern bakery ERP solutions also deliver data-driven insights. They give owners and managers visibility into costs, production trends, and customer demand so they can adjust recipes, manage pricing, and plan marketing campaigns with confidence. Instead of relying on scattered spreadsheets or manual processes, bakeries use ERP software to stay efficient, compliant, and profitable.
Why Bakeries Need Specialized ERP Software: Features to Support Your Business
Running a bakery involves managing perishable goods, complex recipes, and strict compliance standards. General ERP systems rarely address these needs, which is why bakeries benefit from specialized ERP software. The right system supports day-to-day operations, strengthens traceability, and ensures food safety while giving managers visibility into costs and production.
When selecting bakery ERP software, look for features that directly address the realities of your business:
● Inventory management: Track ingredients, packaging, and finished goods in real time. A bakery ERP monitors stock levels across multiple locations, prevents overordering, and alerts staff before ingredients expire.
● Sales and customer management: Connect wholesale, retail, and online sales channels to one system. This centralization allows bakeries to manage customer orders, pricing, discounts, and customer histories without duplication.
● Recipe management: Store recipes, control batch sizes, and manage versioning in a centralized system. Recipe management helps ensure consistency across production runs and links formulas directly to ingredient costs.
● Point-of-sale (POS) functionality: For bakeries with retail outlets, ERP systems with integrated Point of Sale (POS) features record transactions in real time and sync directly with inventory and financial data.
● Financial management: Gain visibility into costs, margins, and profitability by linking production data with accounting. ERP systems for bakeries often include budgeting, cash flow monitoring, and audit-ready financial reports.
● Scheduling and employee management: Plan staff schedules around production runs and retail demand. Some bakery ERP systems include labor tracking tools, allowing managers to allocate resources efficiently and meet peak customer demand.
Top Bakery ERP Software Solutions
Whether you run a commercial bakery with multiple locations or a small artisan shop, the right ERP system keeps production, inventory, and compliance on track. Here’s the list of the best bakery ERP software solutions built to manage recipes, streamline operations, and maintain profitability.
1. Wherefour
Wherefour is a cloud-based ERP designed specifically for food and beverage businesses, including bakeries. It connects inventory, production, compliance, and sales into a single system that helps teams manage operations without relying on spreadsheets or disconnected tools.
Wherefour seamlessly tracks items from start to finish, with details on stock levels, status, costs, and traceability, and provides automatic alerts for reorders, waste, and expiry.
The platform supports compliance with the Food and Drug Administration (FDA), Safe Quality Food (SQF), Hazard Analysis and Critical Control Points (HACCP), and SOC 2 requirements, giving bakeries a structured way to handle audits, and quality checks.
Best for: Wholesale and commercial bakeries that need strong compliance tracking and real-time production oversight.
Features:
● Automatic lot, serial, or barcode sequencing with batch date, facility, or Julian date
● Full traceability, from raw ingredients to finished baked goods
● Custom QA test creation linked to specific stock lots or production runs
● Barcode generation (GS1, Code 128, Code 93) for products and packaging
● Built-in recall reports tied to customers and lots
● Work order-driven production with unit-level cost tracking through accounting integrations
● Direct integrations with Shopify, ShipStation, LeafLink, and SPS Commerce
● Desktop, tablet, or phone accessibility for on-site and remote use
Pricing: Wherefour provides custom price quotes depending on your company’s specific needs.
Schedule a free demo with Wherefour today.
2. Plex
Plex, a Rockwell Automation company, is a manufacturing platform that combines ERP, Manufacturing Execution System (MES), Quality Management System (QMS), and supply chain planning in one system. For bakeries and food manufacturers, Plex supports recipe-driven production, compliance tracking, and end-to-end traceability. It connects plant-floor operations with finance, purchasing, and planning to give a single view of production and supply chain performance.
Best for: Manufacturers that require batch-oriented MES, advanced supply chain planning, and integrated compliance management.
Features:
● Batch-oriented MES for recipe management, yield tracking, and detailed cost reporting
● Scheduling of batch operations across multiple workcenters with in-process quality controls
● Lot tracking and recall management with allergen and origin documentation
● Quality checks across receiving, production, and finished goods with HACCP support
● Real-time plant monitoring with asset performance management and downtime prevention
Pricing: No public pricing is available
3. DEAR Systems
DEAR Systems is a cloud-based ERP designed to unify production, inventory, purchasing, sales, and accounting for manufacturers and distributors. For bakeries, it provides batch and lot tracking, recipe and Bill of Materials (BOM) management, and cost tracking across multiple locations. The platform integrates with e-commerce and accounting solutions to streamline workflows.
Best for: Bakeries that need batch tracking, recipe management, and multi-channel integration for food production.
Features:
● Batch and lot tracking for traceability across multiple locations
● Serial number assignment for warranty and recall management
● Auto Assembly to manage product bundles or kit sets from reserved items
● BOM for recipes, including third-party production and packaging costs
● Real-time inventory management across warehouses and sales channels
Pricing:
- Monthly: ~$600
- Yearly: ~$10,000
4. Katana
Katana is a cloud-based manufacturing ERP that connects production, inventory, and sales in a single platform. It supports food and beverage manufacturers with batch and expiry tracking, recipe management, and material requirements planning. The system integrates directly with e-commerce and accounting tools, giving bakeries visibility across perishable goods, costs, and supply chains.
Best for: Bakeries that sell through e-commerce channels and need direct integration with online stores and accounting systems.
Features:
● Batch and expiry date tracking for perishable goods
● Product recipe and Bill of Materials (BOM) management
● Material requirements planning to align production with availability
● Real-time inventory tracking across multiple items and locations
● Native integrations with Shopify, WooCommerce, QuickBooks Online, and Xero
Pricing:
● Starter plan: From $199/month
● Standard: From $399/month
● Professional: From $899/month
● Add-ons (e.g., warehouse, batch tracking, API access): $199/month or more each
5. Cybake
Cybake is bakery-specific management software that brings wholesale and retail workflows into one system. It covers order capture, production planning, recipe costing, lot tracking, invoicing, deliveries, and returns. Modules support in-store bakery planning for supermarkets and multi-site retailers, while wholesale tools handle standing orders, route planning, and proof-of-delivery. Cybake integrates with accounting platforms, POS/EPOS, labeling and weighing systems, e-commerce, and Electronic Data Interchange (EDI).
Best for: Retail and wholesale bakeries that need in-store planning, online wholesale ordering, and delivery routing with proof-of-delivery.
Features:
● Recipe management and costing with allergens and nutrition data
● Production planning, production reports, picking lists, pricing, and waste control
● Purchasing with goods-in checks, lot tracking, and traceability
● Management reports for operations and compliance
● Customer online ordering portal for wholesale accounts
Pricing: No public pricing is available.
6. JustFood
JustFood is an ERP platform designed for frozen and fresh wholesale bakeries. It provides tools to manage batch production, maintain compliance with global food safety standards, and streamline customer and inventory data. The system combines lot tracking, batch management, and integrated quality audits, offering a single solution to control production and distribution.
Best for: Wholesale bakeries that need ERP with batch tracking, food safety audits, and recipe management.
Features:
● Batch processing and granular lot tracking for traceability
● Recipe and formulation management with bill of materials
● Allergen management with detailed ingredient records
● Mandatory quality checks across production and washdown procedures
● Inventory management with warehouse integration
Pricing: No public pricing is available.
7. Aptean
Aptean focuses on grain-based production, short shelf lives, and strict allergen controls. It centralizes planning, batch execution, traceability, and cost capture for breads, desserts, and other baked goods. The platform includes bakery-specific tools for label control, production touchscreens, and backflushing, plus modules that assign allergens to raw and finished items and alert production teams to upcoming allergen activity. Their forecasting and planning module adds quality and pack-out views with advanced shipment notifications, while detailed costing tracks haulage, labor, machine time, duty, and rework across the supply chain.
Best for: Bakeries that need allergen control, batch execution, traceability, and detailed cost and forecasting.
Features:
● Bakery-specific production tools (label room, optimized production touchscreen, backflushing enhancements)
● Batch and lot tracking for end-to-end traceability and recall readiness
● Allergen assignment for raw materials and finished goods with visibility of upcoming allergen runs
● Collaborative forecasting and planning (quality view, pack-out view, advanced shipment notifications)
● Detailed cost capture for haulage, labor, machinery, duty, and rework
Pricing: No public pricing is available.
8. BatchMaster
BatchMaster is designed to manage bakery operations from ingredient sourcing through packaging and distribution. The system supports recipe and formula management, batch scheduling, quality control, and compliance with FDA and international food standards. It provides tools for costing, allergen labeling, expiration date tracking, and lot traceability across all production stages. BatchMaster handles multiple business models, including private-label, co-packing, and own-brand manufacturing, and integrates with platforms such as QuickBooks, SAP Business One, and Microsoft Dynamics.
Best for: Bakeries that operate across multiple business models and require strong compliance, recipe, and traceability management.
Features:
● Recipe and formulation management with version control
● End-to-end production tracking, from mixing and baking to cooling and packaging
● Batch scheduling and monitoring with yield and cost analysis
● Shelf-life and expiration date management with real-time alerts
● Lot traceability across ingredients, batches, and finished goods
Pricing: No public pricing is available.
9. SAP Business One
SAP Business One is an ERP solution that offers a single platform to manage accounting, purchasing, inventory, production, sales, and customer relationships. The system consolidates data across departments, provides real-time analytics, and supports decision-making with integrated business intelligence. It offers deployment flexibility on-premises or in the cloud and integrates with SAP HANA for faster reporting and advanced analytics.
Best for: Small to mid-sized businesses that require an integrated platform for financials, production, inventory, and customer management.
Features:
● Accounting and financial management with multi-currency support
● Procurement and purchasing with supplier management tools
● Inventory management with lot, serial, and expiry tracking
● Production planning with recipe and batch processing capabilities
● Reporting and analytics powered by SAP HANA integration
Pricing: No public pricing is available.
10. QuickBooks® Commerce
QuickBooks® Commerce is an inventory and order management system that extends the functionality of QuickBooks® Online. It allows businesses to track stock across multiple locations, automate order workflows, and connect directly with e-commerce platforms. The system provides visibility into purchasing, sales, and fulfillment while keeping financial data synchronized with accounting.
Best for: Bakeries that use QuickBooks® Online and need integrated inventory, order, and sales management.
Features:
● Centralized inventory tracking across multiple locations
● Lot and batch tracking for perishable goods
● Automated order workflows from sales to fulfillment
● Supplier and purchase order management
● Sales order and invoice management integrated with QuickBooks Online
Pricing:
● Simple start: $38
● Essentials: $75
● Plus: $115
● Advanced: $275
11. FlexiBake
FlexiBake is a cloud-based ERP platform for bakeries that consolidates recipe management, inventory, production planning, traceability, and wholesale ordering into one system. It supports compliance with SQF audits, automates sales and purchase orders, and integrates with accounting tools like QuickBooks, Xero, and Sage.
Best for: Bakeries that need recipe-level control, automated ordering, and nutritional labeling compliance.
Features:
● Recipe management with automatic costing and yield tracking
● Nutritional analysis and ingredient statement generation for product labeling
● Automated standing sales orders and purchase requisitions
● Production planning with raw material forecasting and staff scheduling
● Forecasting tools for adjusting product pricing based on cost changes
Pricing:
● FlexiBake base: $295/month
● FlexiBake professional: $375/month
● FlexiBake corporate: $495/month
● FlexiBake enterprise: Custom quote
Choose the Right Bakery ERP Software for Your Business
The right ERP system shapes how your bakery manages compliance, traceability, and production. The right software should fit recipe-driven operations, support batch tracking, and help you control perishable goods while preparing your business for future growth.
Wherefour gives bakeries the tools to manage batch and lot traceability, allergen and nutritional data, and regulatory compliance with SOC 2 controls built in. Your team can use it on desktop, tablet, or mobile, whether they’re on the shop floor or working off-site.
The platform connects inventory, scheduling, and quality management directly to your recipes, removing the need for manual workarounds and keeping everything in sync. Real-time production monitoring and accurate inventory tracking help you stay ahead of demand, reduce waste, and remain audit-ready. As your bakery grows, Wherefour scales with you, making it easier to manage multiple locations, simplify compliance, and plan confidently for the future.
Schedule a demo to see how Wherefour supports compliance, traceability, and production.
Best Bakery ERP Software FAQs
What is a bakery inventory management system?
A bakery inventory management system is software that tracks raw ingredients, packaging, and finished goods across your operation. It helps you monitor stock levels in real time, record expiration dates, and manage lot codes so you know exactly what’s on hand and what needs to be reordered.
For bakeries, this type of system goes beyond simple stock tracking. It accounts for perishable goods, supports First In, First Out (FIFO) or First Expired, First Out (FEFO) pulls, and connects inventory directly to recipes and production schedules. That means when you bake a batch of bread, the system automatically deducts flour, yeast, and packaging from stock. It also flags waste, records costs, and generates reports you can use for audits, forecasting, and compliance.
How do bakeries handle inventory?
Bakeries handle inventory by tracking raw materials, packaging supplies, and finished products through systems that account for both perishables and high-volume production. Many bakeries rely on software that connects recipes to stock levels so ingredients automatically adjust as batches are produced. This prevents over-ordering and helps maintain accurate margins.
Inventory is usually managed using methods like FIFO or FEFO to reduce spoilage and ensure compliance. Bakeries also monitor expiration dates, record lot numbers for traceability, and run regular counts to keep the system accurate. Larger bakeries may integrate inventory management with purchasing, production scheduling, and sales so all departments work from the same real-time data.
What are the challenges in bakery inventory management?
Bakery inventory management is challenging because products are highly perishable, and raw ingredients often have short shelf lives. Tracking expiration dates, lot numbers, and allergens requires precision to avoid spoilage, waste, or compliance issues. Small mistakes can result in lost revenue or costly recalls.
Another challenge is balancing supply and demand. Bakeries must forecast accurately to meet customer orders without overproducing. Seasonal demand swings, fluctuating ingredient prices, and multiple sales channels add complexity. Coordinating recipes, production runs, and supplier deliveries through manual methods like spreadsheets makes errors more likely, which is why many bakeries adopt ERP systems to maintain traceability and control.
Can bakery inventory management software control expiration dates for bakery products?
Yes. Bakery inventory management software typically includes batch and lot tracking tools that monitor expiration dates for both raw ingredients and finished goods. The system records shelf life when materials arrive, assigns expiry information during production, and triggers alerts as products near their end dates.
This visibility helps bakeries rotate stock properly, follow FIFO or FEFO methods, and ensure expired goods never reach customers. It also supports compliance by keeping digital records for audits and food safety checks. Instead of relying on manual logs, bakeries can automate expiration tracking to reduce waste and protect product quality.
What is the best bakery system?
The best bakery system depends on your size, product mix, and compliance requirements. A small artisan bakery may need software that focuses on recipe costing, order management, and expiration tracking, while larger wholesale operations require advanced features like production scheduling, quality control, and regulatory compliance.
Wherefour is the best bakery ERP system because it manages batch and lot traceability, allergen and nutritional data, and regulatory requirements in one platform. It also supports inventory accuracy and integrates with accounting tools, giving bakeries visibility across operations while reducing the need for custom workarounds.
Beyond these core features, Wherefour offers audit-ready recall reports, automated alerts for expiring products, and seamless e-commerce integrations. Bakeries can also customize lot codes, streamline label printing, and provide wholesale customers with a self-service portal, all in a single, cloud-based solution. This combination of compliance, traceability, and operational flexibility makes Wherefour a proven choice for bakeries that want software built specifically for their industry.