Aim: Position paper on endpoints of active periodontal therapy for designing treatment guidelines. The question was as follows: How are, for an individual patient, commonly applied periodontal probing measures—recorded after active periodontal therapy—related to (a) stability of clinical attachment level, (b) tooth survival, (c) need for re-treatment or (d) oral health-related quality of life. Methods: A literature search was conducted in Ovid MEDLINE(R) and Epub Ahead of Print, In-Process & Other Non-Indexed Citations and Daily <1946 to 07 June 2019>. Results: A total of 94 papers were retrieved. From the literature search, it was found that periodontitis patients with a low proportion of deep residual pockets after active periodontal therapy are more likely to have stability of clinical attachment level over a follow-up time of ≥1 year. Other supporting literature confirms this finding and additionally reports, at the patient level, that probing pocket depths ≥6 mm and bleeding on probing scores ≥30% are risks for tooth loss. There is lack of evidence that periodontal probing measures after completion of active periodontal treatment are tangible to the patient. Conclusions: Based on literature and biological plausibility, it is reasonable to state that periodontitis patients with a low proportion of residual periodontal pockets and little inflammation are more likely to have stability of clinical attachment levels and less tooth loss over time. Guidelines for periodontal therapy should take into consideration (a) long-term tangible patient outcomes, (b) that shallow pockets (≤4 mm) without bleeding on probing in patients with <30% bleeding sites are the best guarantee for the patient for stability of his/her periodontal attachment, (c) patient heterogeneity and patient changes in immune response over time, and (d) that treatment strategies include lifestyle changes of the patient. Long-term large population-based and practice-based studies on the efficacy of periodontal therapies including both clinical and patient-reported outcomes (PROs) need to be initiated, which include the understanding that periodontitis is a complex disease with variation of inflammatory responses due to environment, (epi)genetics, lifestyle and ageing. Involving people living with periodontitis as co-researchers in the design of these studies would also help to improve their relevance.