We study the positivity of sequences $f$ that satisfy a third-order holonomic recurrence $f(n+3)= P_2(n) f(n+2) + P_1(n) f(n+1) + P_0(n) f(n)$ whose coefficients $P_0$, $P_1$ and $P_2$ are rational functions in $\R(x)$. We provide a sufficient condition on $P_0$, $P_1$ and $P_2$ for the recurrence to admit a solution all but finitely many terms of which are positive, and whose positivity is robust under small perturbations of the initial values. This sufficient condition is also a necessary condition for a subclass of the recurrences. By developing the proof of this sufficient condition, for another subclass of the recurrences, we show that it is decidable whether all the terms of a given sequence are positive for any initial values outside an exceptional plane. It is common to construct a positivity certificate, which guarantees the positivity of a solution, to show this kind of decidability. In this paper, we construct a new type of positivity certificate via the $S$-scaled difference $f(n+1) - S(n) f(n)$ for a suitable $S \in \R(x)$. This result partially improves the work by Ibrahim and Salvy.

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