Short version — which to pick

• QuickBooks Bill Pay: Best if you already use QuickBooks Online, pay a relatively small number of bills, and want a native, lower‑cost option with automatic posting into your books. QuickBooks Bill Pay Basic is now included with QBO and gives a few free ACH payments each month; Premium/Elite add higher ACH allowances, approval workflows and unlimited 1099 filing. (quickbooks.intuit.com)
• Bill.com (BILL): Best if you run higher‑volume or more complex AP (multi‑entity, PO/2‑ or 3‑way matching, many approvers/signers), need a vendor/payment network, virtual card capabilities, or must integrate with multiple ERPs (QuickBooks Desktop, NetSuite, Sage, etc.). BILL is a separate, more full‑featured AP automation platform with per‑user pricing and per‑transaction fees. (bill.com)

Quick practical comparison (high‑impact points)

• Integration and workflow
  • QuickBooks Bill Pay: native to QBO — payments, bills and matches live inside QuickBooks with automatic recording and reconciliation. Good for simple AP flows inside QBO. (quickbooks.intuit.com)
  • Bill.com: purpose‑built AP/AR platform with 2‑way sync to many accounting systems (QBO, QuickBooks Desktop, NetSuite, Sage Intacct, etc.), advanced approval workflows, PO matching and supplier network features. Better for complex workflows or multi‑ERP environments. (bill.com)
• Pricing model (examples)
  • QuickBooks Bill Pay: Basic plan is included with QBO (gives a small number of free ACH payments). Paid Bill Pay Premium/Elite tiers add more ACH allotments and advanced controls; price depends on the QBO/Bill Pay plan you choose. (QuickBooks shows promotional pricing on Premium/Elite in some markets.) (quickbooks.intuit.com)
  • Bill.com: per‑user monthly plans (examples on BILL’s site: Essentials/Team/Corporate/Enterprise tiers — starting around $45/user/month for higher tiers; exact tiers and discounts vary). Bill.com also charges transaction fees (ACH $0.59, mailed check $1.99, virtual card often free to you if vendor accepts, faster ACH/check fees for expedited delivery, etc.). Account and per‑transaction fees can add up depending on volume and payment types. (bill.com)
• Payment types & fees
  • Both support ACH and mailed checks. Both support faster/expedited payments for extra fees.
  • Bill.com has explicit per‑payment fees listed (ACH $0.59, mailed check $1.99, instant/faster fees and card/FX fees). QuickBooks Bill Pay includes some free ACH in Basic and charges for faster ACH/checks; limits and fee details are published by Intuit and vary by plan. Compare your expected monthly ACH/check/card counts to the fees. (bill.com)
• Vendor network & virtual cards
  • Bill.com advertises a large vendor network and virtual card capability (useful for earning card rewards and paying vendors that accept card payments). QuickBooks also promotes its QuickBooks Business Network and electronic options, but Bill.com’s independent network and virtual card program may be broader for non‑QBO ecosystems. (bill.com)
• Support & reliability (real‑user signals)
  • Public reviews show mixed experiences: many customers praise Bill.com’s automation and features but some report frustrating customer‑support and hold/verification issues; QuickBooks Bill Pay users report the convenience of the native flow but also occasional issues with limits, scheduling, or timing. Read current reviews and ask both vendors about SLA/support for your plan. (capterra.com)

Which one for your situation (recommendations)

• Use QuickBooks Bill Pay if:
  • You run QuickBooks Online and you want the simplest, lowest‑friction option.
  • You pay a handful of bills monthly or don’t need advanced AP workflows/PO matching.
  • You want payments to post automatically inside QBO without a separate app. (quickbooks.intuit.com)
• Use Bill.com if:
  • You have higher AP volume, multiple approvers/signers, multi‑entity needs or need PO/2‑ or 3‑way matching.
  • You need broader ERP integrations (NetSuite, Sage Intacct, Desktop QuickBooks) or a larger vendor/payment network and virtual card support.
  • You’re willing to pay per‑user subscription and per‑transaction fees in exchange for richer automation and controls. (bill.com)

Quick checklist to decide (do these before switching)

• Count your monthly payment volume by type (ACH/check/card) and estimate transaction fees under both services.
• Confirm whether your vendors accept virtual card payments (if you plan to use cards).
• If you use QuickBooks Online, enable Bill Pay Basic and test the workflow first — it may be sufficient and lower cost. (quickbooks.intuit.com)
• If you need advanced workflows, request a Bill.com demo and ask about 2‑way sync, multi‑entity support, PO matching, and live examples from similar customers. (bill.com)
• Ask both vendors for exact fee quotes and ACH/check speed/limits for your account size to avoid surprises.

If you want, I can:

• Run a side‑by‑side cost estimate for your expected monthly volume (you give typical counts and amounts for ACH/checks/cards), or
• Summarize the exact Bill Pay plan/transaction limits and fees for a specific QuickBooks subscription level you have.

Sources (high‑impact references used)

• QuickBooks Bill Pay product & plans documentation. (quickbooks.intuit.com)
• Bill.com pricing, transaction fees and integration documentation. (bill.com)
• Independent comparisons & user reviews (FitSmallBusiness, Capterra / user forums) for real‑world pros/cons and pricing context. (fitsmallbusiness.com)

Would you like me to estimate the monthly cost for both options using your real monthly volumes (ACH/check/card counts and number of users)?