A major issue with the WooCommerce Deposits plugin is that it does not support automatic recurring payments. For example, the first payment goes through as a deposit but the remaining payments are not automatically charged to the customer’s payment method on file.

The customer then has to manually go and make the payment. The WooCommerce Payment Plans for Subscriptions plugin, on the other hand, is automated, as the remaining payments in the customer’s plan are automatically charged to the customer’s payment method (such as a credit card or PayPal) using their chosen payment method

The WooCommerce Deposits plugin is good at what it’s intended for: allowing your customers to place an initial deposit on a product and then paying the rest when they have the money, at which time you ship the product. But if you want to charge your customers installments, you need WooCommerce Payments Plans for Subscriptions.