As pointed out by @DavidPurton in a comment, the documentation of mathastext indicates (but in a not so clear way) that upgreek option has effect only if one of the Greek related options described in §1.9 Greek letters is active.
For example:
\documentclass{article}
\usepackage[upgreek, LGRgreek]{mathastext}
\usepackage{bm}
\begin{document}
\[\phi, \Phi\]
\[\bm{\phi}, \bm{\Phi}\]
\end{document}
Output:

However, perhaps your font set-up has some specifics.
Other approaches
E.g. you could use \usepackage[upright]{fourier}...load text packages...\usepackage{mathastext} to benefit from the Fourier set-up for Greek letters. Then \bm{\phi} gives a bold upright Greek letter. mathastext does not interfere at all in this.
\documentclass{article}
\usepackage[upright]{fourier}
% add here text packages according to what is needed
\usepackage{mathastext}% does not modify anything to Greek in math
\usepackage{bm}
\begin{document}
\[\phi, \Phi\]
\[\bm{\phi}, \bm{\Phi}\]
\end{document}
Produces:

Or use eulergreek option:
\documentclass{article}
\usepackage[eulergreek]{mathastext}
\usepackage{bm}
\begin{document}
\[\phi, \Phi\]
\[\bm{\phi}, \bm{\Phi}\]
\end{document}
Produces:

upgreekoption only does something if you also use theLGRgreekoption. But this changes the shape of the phi which might not be what you want. – David Purton Sep 07 '17 at 03:02upgreekpackage an option for you? If so, you could simply type\bm{\upphi}. – Mico Sep 07 '17 at 04:26eulergreekandsymbolgreekofmathastextuse same glyphs asupgreekpackage, but with\phi, not\upphi. So if one needs both\phiand\upphiit is better to useupgreekpackage. If not one can just pass one ofeulergreekorsymbolgreekoption tomathastext. Then\MTEulerScaleand\MTSymbolScalecommands allow to scale the fonts (whereupgreekonly provides one alternative scale for Symbol font). – Sep 07 '17 at 09:28