<p>We generalise a method recently introduced in the literature, that derives canonical differential equations, to multi-scale Feynman integrals with an underlying Calabi-Yau geometry. We start by recomputing a canonical form for the sunrise integral with all unequal masses. Additionally, we compute for the first time a canonical form for the three-loop banana integral with two unequal masses and for a four-loop banana integral with two unequal masses. For the integrals we compute, we find an <i>ϵ</i>-form whose connection has at most simple poles. We motivate our construction by studying the Picard-Fuchs operators acting on the integrals considered. In the appendices, we give a constructive explanation for why our generalisation works.</p>