I am not a Jira Portfolio expert, but here is my perspective at a high level. I hope this helps.
Jira Portfolio is fundamentally built on top of Jira, while Jira Align is a completely independent application (albeit being integrated with Jira) which communicates/integrates with Jira via the Atlassian Jira API.
What this means is that Jira Portfolio depends (for the most part) on the underlying Jira data structure, which is not normalized and is focused on the issue (due to Jira's issue management/bug tracking origins) and not the team or the time dimensions essential to proper agile discipline. This means (stand-alone) Portfolio is also missing most SAFe constructs, such as multiple team levels, time dimensions, objectives, and a bunch more. Portfolio basically gives you the ability to add higher-level work objects above the Jira Epic (and some road mapping/planning), but there are still no time planning dimensions above the sprint that are meaningful (such as SAFe's Program Increment). There are actually also no meaningful teams in Jira, and that impacts how teams roll up (or don't) in Portfolio.
Jira Align has a (mostly) normalized data structure that is based on agile and agile at scale (think SAFe) core principles and concepts that allow for organizations to properly plan, monitor, and execute work over multiple time dimensions and scale (from strategic to tactical).
Dimensions within Jira Align, mostly missing from Jira and Portfolio, include:
For example, a story must be completed by a single team in a sprint or be split (hence sprints bound stories from a time perspective and teams from an org perspective). That story is ideally parented to a feature (Jira Epic) that is parented to a Portfolio Epic (also known by many as an initiative). The initiative may be linked to a strategic theme that allows tracking ROI and spend based on strategic budgets. The agile team working the story rolls up to an agile release train (also known as an ART or program), which in turn rolls up to a portfolio with its own team. Time-wise, the sprint is contained within the larger Program Increment and the time frame of the portfolio epic (which can be several PIs). All of these dimensions (and more) are available out of the box with Jira Align, and can be reported against.
The major integration difference between the two, in my opinion, is that Jira Align connects with Jira via the Atlassian Jira API, while Portfolio is an extension of Jira. This means that to get meaningful metrics and roll-ups in Jira Align requires most teams to change behavior in Jira to a more normalized, organizational standard vs each team having any workflow, create/edit screen, custom fields, etc. that they might be use to in Jira without Jira Align.
Due to recent challenges of most companies having to move to virtual and remote PI planning events, the Jira Align Solutions Architects wanted to start to capture some best practices and FAQ Table of...
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