The best HR & payroll software for marketing agencies
A marketing agency rarely has a tidy roster of salaried staff. It runs on a blend: W-2 employees (your core payroll), 1099 contractors and freelancers (designers, writers, developers) who flex with the work, and increasingly some of them are overseas. The feature that decides the tool is how cleanly it pays that mixed team — full payroll for employees, simple contractor payouts, and ideally international contractors — without forcing you into two systems. We reweighted the rubric around the blended team and ranked the six.
We scored the same five criteria as our main HR and payroll ranking, then reweighted for an agency. The deciding criterion is paying a blended workforce — employees plus domestic and international contractors — weighted at 30%. We kept benefits administration high because it helps agencies retain talent, valued ease and fast onboarding for a small back office, weighted integrations with time-tracking and project tools (agencies bill by the hour), and held value steady. See the full rubric →
Blended payroll & contractors30%
Benefits administration20%
Ease & onboarding20%
Integrations (time/PM)15%
Value15%
01
RANK
★ Editor’s Choice
Gusto
Best for most agencies
The right default for a small-to-mid agency. Gusto runs full-service payroll for your W-2 employees — taxes filed automatically — and pays 1099 contractors in the same system, so one tool covers the whole team. It handles health benefits, offers, onboarding and time tracking, and a founder can operate it without a payroll specialist. At $49 a month plus $6 per person to start, it is priced for a lean back office. For agencies hiring only in the US, this is the rational choice.
The moment an agency hires a designer in Lisbon or a developer in Manila, Deel becomes the answer. It handles compliant contractor agreements and payments in 150-plus countries, and can formally employ people abroad through its Employer of Record service so you do not have to open a foreign entity. Domestic contractor management runs about $49 per person a month; the EOR service starts around $599 per employee. Pair it with a US payroll tool rather than treating it as your whole stack.
The most powerful platform here, joining HR, payroll, IT and app provisioning in one system — genuinely useful when an agency is scaling and tired of disconnected tools and manual laptop setups for new hires. It pays employees and contractors, including internationally. The trade-offs are modular pricing that is quote-gated and a platform heavier than a ten-person shop needs; it earns its keep as you grow past that.
Justworks is a PEO (Professional Employer Organisation) — it co-employs your team so a small agency can offer big-company health and benefits packages, with payroll and compliance handled for you. That is its strength: access to strong benefits at small scale. The model charges per employee (PEO Basic around $79 a head), so it fits agencies with a solid core of employees, less so a roster that is mostly contractors.
BambooHR is the best people-management system here — hiring, onboarding, records, performance and time off in one tidy place that staff actually enjoy using. The honest caveat is that it is an HRIS first; payroll is an add-on, not its core. Run it alongside a dedicated payroll tool and it shines; buy it expecting full payroll and you will be disappointed. Pricing is quote-based, roughly $10 to $17 per employee a month.
Paychex Flex is the most established, compliance-heavy option, with a dedicated payroll specialist and deep coverage for taxes, filings and HR services across all states. That hand-holding suits an agency that wants payroll truly off its plate. The downsides are a dated interface and quote-based pricing with per-run fees, so the real cost is higher than the $47-a-month headline suggests.
What is the simplest tool to pay both employees and freelancers?+
Gusto. It runs full-service payroll for your W-2 employees and pays 1099 contractors in the same system, so you are not juggling two tools or exporting spreadsheets. A founder can operate it without hiring a payroll specialist, which is exactly what most agencies want.
How do I pay contractors who live abroad?+
Use Deel. It handles compliant agreements and payments for contractors in 150-plus countries, and can formally employ someone overseas through its Employer of Record service so you avoid setting up a foreign company. Most agencies pair Deel for international hires with a US payroll tool like Gusto for the domestic team.
What is a PEO, and is it right for an agency?+
A PEO (Professional Employer Organisation) like Justworks co-employs your team, which lets a small agency offer large-company health and benefits packages and offloads compliance. It charges per employee, so it makes sense when you have a solid core of W-2 staff you want to retain with strong benefits — less so if most of your roster is contractors.
Can BambooHR run my payroll?+
Not on its own as its main job. BambooHR is an HRIS — built for hiring, onboarding, records and time off — and payroll is an add-on rather than its core strength. It works best paired with a dedicated payroll tool. If payroll is your primary need, start with Gusto or Rippling instead.